diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml index 0aa0c8c23..6bb758898 100644 --- a/.github/workflows/cicd.yml +++ b/.github/workflows/cicd.yml @@ -28,6 +28,8 @@ jobs: args: --extend-ignore E501,E741 - name: Run Tests + # We don't have access to secrets when the PR is created from a fork + if: ${{ github.ref == 'refs/heads/master' && github.repository == 'FHIR/genomics-operations' }} run: ./fetch_utilities_data.sh && python -m pytest env: MONGODB_READONLY_PASSWORD: ${{ secrets.MONGODB_READONLY_PASSWORD }} diff --git a/tests/expected_outputs/find_population_dx_implications/1.json b/tests/expected_outputs/find_population_dx_implications/1.json index 81072f5cd..19c8b2800 100644 --- a/tests/expected_outputs/find_population_dx_implications/1.json +++ b/tests/expected_outputs/find_population_dx_implications/1.json @@ -1,19 +1,18 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "implications", "part": [ { - "name": "numerator", + "name": "denominator", "valueQuantity": { - "value": 5 + "value": 1116 } }, { - "name": "denominator", + "name": "numerator", "valueQuantity": { - "value": 1116 + "value": 5 } }, { @@ -38,5 +37,6 @@ } ] } - ] -} + ], + "resourceType": "Parameters" +} \ No newline at end of file diff --git a/tests/expected_outputs/find_population_dx_implications/2.json b/tests/expected_outputs/find_population_dx_implications/2.json index 355dabda2..d49b982f9 100644 --- a/tests/expected_outputs/find_population_dx_implications/2.json +++ b/tests/expected_outputs/find_population_dx_implications/2.json @@ -1,22 +1,22 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "implications", "part": [ { - "name": "numerator", + "name": "denominator", "valueQuantity": { - "value": 13 + "value": 1116 } }, { - "name": "denominator", + "name": "numerator", "valueQuantity": { - "value": 1116 + "value": 13 } } ] } - ] -} + ], + "resourceType": "Parameters" +} \ No newline at end of file diff --git a/tests/expected_outputs/find_population_dx_implications/3.json b/tests/expected_outputs/find_population_dx_implications/3.json index 81072f5cd..19c8b2800 100644 --- a/tests/expected_outputs/find_population_dx_implications/3.json +++ b/tests/expected_outputs/find_population_dx_implications/3.json @@ -1,19 +1,18 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "implications", "part": [ { - "name": "numerator", + "name": "denominator", "valueQuantity": { - "value": 5 + "value": 1116 } }, { - "name": "denominator", + "name": "numerator", "valueQuantity": { - "value": 1116 + "value": 5 } }, { @@ -38,5 +37,6 @@ } ] } - ] -} + ], + "resourceType": "Parameters" +} \ No newline at end of file diff --git a/tests/expected_outputs/find_population_dx_implications/4.json b/tests/expected_outputs/find_population_dx_implications/4.json index 5bd256445..d408a7046 100644 --- a/tests/expected_outputs/find_population_dx_implications/4.json +++ b/tests/expected_outputs/find_population_dx_implications/4.json @@ -1,19 +1,18 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "implications", "part": [ { - "name": "numerator", + "name": "denominator", "valueQuantity": { - "value": 18 + "value": 1116 } }, { - "name": "denominator", + "name": "numerator", "valueQuantity": { - "value": 1116 + "value": 18 } }, { @@ -90,5 +89,6 @@ } ] } - ] -} + ], + "resourceType": "Parameters" +} \ No newline at end of file diff --git a/tests/expected_outputs/find_population_molecular_consequences/1.json b/tests/expected_outputs/find_population_molecular_consequences/1.json index 3aa654cca..c840c83dc 100644 --- a/tests/expected_outputs/find_population_molecular_consequences/1.json +++ b/tests/expected_outputs/find_population_molecular_consequences/1.json @@ -1,26 +1,26 @@ { - "resourceType": "Parameters", - "parameter": [ - { - "name": "consequences", - "part": [ + "parameter": [ { - "name": "numerator", - "valueQuantity": { - "value": 1 - } - }, - { - "name": "denominator", - "valueQuantity": { - "value": 1116 - } - }, - { - "name": "subject", - "valueString": "TCGA-DD-A1EH" + "name": "consequences", + "part": [ + { + "name": "denominator", + "valueQuantity": { + "value": 1116 + } + }, + { + "name": "numerator", + "valueQuantity": { + "value": 1 + } + }, + { + "name": "subject", + "valueString": "TCGA-DD-A1EH" + } + ] } - ] - } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_population_specific_haplotypes/1.json b/tests/expected_outputs/find_population_specific_haplotypes/1.json index 063790a68..60d98624d 100644 --- a/tests/expected_outputs/find_population_specific_haplotypes/1.json +++ b/tests/expected_outputs/find_population_specific_haplotypes/1.json @@ -1,30 +1,30 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ { - "name": "variantItem", - "valueString": "CYP2C9 *1/*2" - }, - { - "name": "numerator", + "name": "denominator", "valueQuantity": { - "value": 1 + "value": 1116 } }, { - "name": "denominator", + "name": "numerator", "valueQuantity": { - "value": 1116 + "value": 1 } }, { "name": "subject", "valueString": "NB6TK328" + }, + { + "name": "variantItem", + "valueString": "CYP2C9 *1/*2" } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_population_specific_haplotypes/2.json b/tests/expected_outputs/find_population_specific_haplotypes/2.json index cbfa58ac9..40c11710f 100644 --- a/tests/expected_outputs/find_population_specific_haplotypes/2.json +++ b/tests/expected_outputs/find_population_specific_haplotypes/2.json @@ -1,23 +1,18 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ { - "name": "variantItem", - "valueString": "CYP2C19" - }, - { - "name": "numerator", + "name": "denominator", "valueQuantity": { - "value": 1032 + "value": 1116 } }, { - "name": "denominator", + "name": "numerator", "valueQuantity": { - "value": 1116 + "value": 1032 } }, { @@ -4147,8 +4142,13 @@ { "name": "subject", "valueString": "tacro9" + }, + { + "name": "variantItem", + "valueString": "CYP2C19" } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_population_specific_haplotypes/3.json b/tests/expected_outputs/find_population_specific_haplotypes/3.json index fe6e8fe7f..578323507 100644 --- a/tests/expected_outputs/find_population_specific_haplotypes/3.json +++ b/tests/expected_outputs/find_population_specific_haplotypes/3.json @@ -1,9 +1,14 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "haplotypes", "part": [ + { + "name": "denominator", + "valueQuantity": { + "value": 1116 + } + }, { "name": "haplotypeItem", "valueString": "HLA-A*01 AND HLA-B*08 AND HLA-DRB1*03" @@ -14,17 +19,12 @@ "value": 1 } }, - { - "name": "denominator", - "valueQuantity": { - "value": 1116 - } - }, { "name": "subject", "valueString": "NB6TK328" } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_population_specific_haplotypes/4.json b/tests/expected_outputs/find_population_specific_haplotypes/4.json index b579aafef..33babb996 100644 --- a/tests/expected_outputs/find_population_specific_haplotypes/4.json +++ b/tests/expected_outputs/find_population_specific_haplotypes/4.json @@ -1,19 +1,8 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ - { - "name": "variantItem", - "valueString": "HLA-A*01" - }, - { - "name": "numerator", - "valueQuantity": { - "value": 5 - } - }, { "name": "denominator", "valueQuantity": { @@ -21,24 +10,18 @@ } }, { - "name": "subject", - "valueString": "L2345" + "name": "numerator", + "valueQuantity": { + "value": 1 + } }, { "name": "subject", "valueString": "NB6TK328" }, { - "name": "subject", - "valueString": "XYZ123" - }, - { - "name": "subject", - "valueString": "XYZ234" - }, - { - "name": "subject", - "valueString": "XYZ345" + "name": "variantItem", + "valueString": "HLA-B*08" } ] }, @@ -46,24 +29,28 @@ "name": "variants", "part": [ { - "name": "variantItem", - "valueString": "HLA-B*08" - }, - { - "name": "numerator", + "name": "denominator", "valueQuantity": { - "value": 1 + "value": 1116 } }, { - "name": "denominator", + "name": "numerator", "valueQuantity": { - "value": 1116 + "value": 2 } }, { "name": "subject", "valueString": "NB6TK328" + }, + { + "name": "subject", + "valueString": "XYZ234" + }, + { + "name": "variantItem", + "valueString": "HLA-DRB1*03" } ] }, @@ -71,30 +58,43 @@ "name": "variants", "part": [ { - "name": "variantItem", - "valueString": "HLA-DRB1*03" + "name": "denominator", + "valueQuantity": { + "value": 1116 + } }, { "name": "numerator", "valueQuantity": { - "value": 2 + "value": 5 } }, { - "name": "denominator", - "valueQuantity": { - "value": 1116 - } + "name": "subject", + "valueString": "L2345" }, { "name": "subject", "valueString": "NB6TK328" }, + { + "name": "subject", + "valueString": "XYZ123" + }, { "name": "subject", "valueString": "XYZ234" + }, + { + "name": "subject", + "valueString": "XYZ345" + }, + { + "name": "variantItem", + "valueString": "HLA-A*01" } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_population_specific_variants/1.json b/tests/expected_outputs/find_population_specific_variants/1.json index bdbfee1b4..9adffd61a 100644 --- a/tests/expected_outputs/find_population_specific_variants/1.json +++ b/tests/expected_outputs/find_population_specific_variants/1.json @@ -1,12 +1,13 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ { - "name": "variantItem", - "valueString": "NC_000011.10:g.8263343T>C AND NC_000006.11:26091305:T:C" + "name": "denominator", + "valueQuantity": { + "value": 1116 + } }, { "name": "numerator", @@ -15,12 +16,11 @@ } }, { - "name": "denominator", - "valueQuantity": { - "value": 1116 - } + "name": "variantItem", + "valueString": "NC_000011.10:g.8263343T>C AND NC_000006.11:26091305:T:C" } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_population_specific_variants/2.json b/tests/expected_outputs/find_population_specific_variants/2.json index eb8fb18e6..898386e4e 100644 --- a/tests/expected_outputs/find_population_specific_variants/2.json +++ b/tests/expected_outputs/find_population_specific_variants/2.json @@ -1,23 +1,18 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ { - "name": "variantItem", - "valueString": "NC_000001.10:144931726:G:A AND NC_000001.10:145532548:T:C AND NC_000001.10:145592072:A:T" - }, - { - "name": "numerator", + "name": "denominator", "valueQuantity": { - "value": 6 + "value": 1116 } }, { - "name": "denominator", + "name": "numerator", "valueQuantity": { - "value": 1116 + "value": 6 } }, { @@ -43,8 +38,13 @@ { "name": "subject", "valueString": "NA19240" + }, + { + "name": "variantItem", + "valueString": "NC_000001.10:144931726:G:A AND NC_000001.10:145532548:T:C AND NC_000001.10:145592072:A:T" } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_population_structural_intersecting_variants/1.json b/tests/expected_outputs/find_population_structural_intersecting_variants/1.json index a2bf0551f..e6b1d3e15 100644 --- a/tests/expected_outputs/find_population_structural_intersecting_variants/1.json +++ b/tests/expected_outputs/find_population_structural_intersecting_variants/1.json @@ -1,12 +1,13 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ { - "name": "rangeItem", - "valueString": "NC_000022.10:42522500-42526812" + "name": "denominator", + "valueQuantity": { + "value": 1116 + } }, { "name": "numerator", @@ -15,10 +16,8 @@ } }, { - "name": "denominator", - "valueQuantity": { - "value": 1116 - } + "name": "rangeItem", + "valueString": "NC_000022.10:42522500-42526812" }, { "name": "subject", @@ -34,5 +33,6 @@ } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_population_structural_intersecting_variants/2.json b/tests/expected_outputs/find_population_structural_intersecting_variants/2.json index 655050eb8..214967929 100644 --- a/tests/expected_outputs/find_population_structural_intersecting_variants/2.json +++ b/tests/expected_outputs/find_population_structural_intersecting_variants/2.json @@ -1,12 +1,13 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ { - "name": "rangeItem", - "valueString": "NC_000017.11:43044294-43125364" + "name": "denominator", + "valueQuantity": { + "value": 1116 + } }, { "name": "numerator", @@ -15,10 +16,8 @@ } }, { - "name": "denominator", - "valueQuantity": { - "value": 1116 - } + "name": "rangeItem", + "valueString": "NC_000017.11:43044294-43125364" } ] }, @@ -26,8 +25,10 @@ "name": "variants", "part": [ { - "name": "rangeItem", - "valueString": "NC_000013.11:32315507-32400268" + "name": "denominator", + "valueQuantity": { + "value": 1116 + } }, { "name": "numerator", @@ -36,10 +37,8 @@ } }, { - "name": "denominator", - "valueQuantity": { - "value": 1116 - } + "name": "rangeItem", + "valueString": "NC_000013.11:32315507-32400268" }, { "name": "subject", @@ -47,5 +46,6 @@ } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_population_structural_intersecting_variants/3.json b/tests/expected_outputs/find_population_structural_intersecting_variants/3.json index a2bf0551f..e6b1d3e15 100644 --- a/tests/expected_outputs/find_population_structural_intersecting_variants/3.json +++ b/tests/expected_outputs/find_population_structural_intersecting_variants/3.json @@ -1,12 +1,13 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ { - "name": "rangeItem", - "valueString": "NC_000022.10:42522500-42526812" + "name": "denominator", + "valueQuantity": { + "value": 1116 + } }, { "name": "numerator", @@ -15,10 +16,8 @@ } }, { - "name": "denominator", - "valueQuantity": { - "value": 1116 - } + "name": "rangeItem", + "valueString": "NC_000022.10:42522500-42526812" }, { "name": "subject", @@ -34,5 +33,6 @@ } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_population_structural_subsuming_variants/1.json b/tests/expected_outputs/find_population_structural_subsuming_variants/1.json index cc94b763a..71c9d831c 100644 --- a/tests/expected_outputs/find_population_structural_subsuming_variants/1.json +++ b/tests/expected_outputs/find_population_structural_subsuming_variants/1.json @@ -1,12 +1,13 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ { - "name": "rangeItem", - "valueString": "NC_000022.10:42522500-42526812" + "name": "denominator", + "valueQuantity": { + "value": 1116 + } }, { "name": "numerator", @@ -15,12 +16,11 @@ } }, { - "name": "denominator", - "valueQuantity": { - "value": 1116 - } + "name": "rangeItem", + "valueString": "NC_000022.10:42522500-42526812" } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_population_structural_subsuming_variants/2.json b/tests/expected_outputs/find_population_structural_subsuming_variants/2.json index eaf7f617f..9e8438afb 100644 --- a/tests/expected_outputs/find_population_structural_subsuming_variants/2.json +++ b/tests/expected_outputs/find_population_structural_subsuming_variants/2.json @@ -1,12 +1,13 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ { - "name": "rangeItem", - "valueString": "NC_000017.10:37844346-37884911" + "name": "denominator", + "valueQuantity": { + "value": 1116 + } }, { "name": "numerator", @@ -15,10 +16,8 @@ } }, { - "name": "denominator", - "valueQuantity": { - "value": 1116 - } + "name": "rangeItem", + "valueString": "NC_000017.10:37844346-37884911" } ] }, @@ -26,8 +25,10 @@ "name": "variants", "part": [ { - "name": "rangeItem", - "valueString": "NC_000007.13:116312249-116438431" + "name": "denominator", + "valueQuantity": { + "value": 1116 + } }, { "name": "numerator", @@ -36,10 +37,8 @@ } }, { - "name": "denominator", - "valueQuantity": { - "value": 1116 - } + "name": "rangeItem", + "valueString": "NC_000007.13:116312249-116438431" }, { "name": "subject", @@ -47,5 +46,6 @@ } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_population_tx_implications/2.json b/tests/expected_outputs/find_population_tx_implications/2.json index 3c7ceec93..19f4bcf26 100644 --- a/tests/expected_outputs/find_population_tx_implications/2.json +++ b/tests/expected_outputs/find_population_tx_implications/2.json @@ -1,19 +1,18 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "implications", "part": [ { - "name": "numerator", + "name": "denominator", "valueQuantity": { - "value": 1035 + "value": 1116 } }, { - "name": "denominator", + "name": "numerator", "valueQuantity": { - "value": 1116 + "value": 1035 } }, { @@ -4158,5 +4157,6 @@ } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_population_tx_implications/3.json b/tests/expected_outputs/find_population_tx_implications/3.json index 0d597a629..c232cc579 100644 --- a/tests/expected_outputs/find_population_tx_implications/3.json +++ b/tests/expected_outputs/find_population_tx_implications/3.json @@ -1,19 +1,18 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "implications", "part": [ { - "name": "numerator", + "name": "denominator", "valueQuantity": { - "value": 1 + "value": 1116 } }, { - "name": "denominator", + "name": "numerator", "valueQuantity": { - "value": 1116 + "value": 1 } }, { @@ -22,5 +21,6 @@ } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_population_tx_implications/4.json b/tests/expected_outputs/find_population_tx_implications/4.json index 6b0518c62..59c889313 100644 --- a/tests/expected_outputs/find_population_tx_implications/4.json +++ b/tests/expected_outputs/find_population_tx_implications/4.json @@ -1,19 +1,18 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "implications", "part": [ { - "name": "numerator", + "name": "denominator", "valueQuantity": { - "value": 103 + "value": 1116 } }, { - "name": "denominator", + "name": "numerator", "valueQuantity": { - "value": 1116 + "value": 103 } }, { @@ -430,5 +429,6 @@ } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_population_tx_implications/5.json b/tests/expected_outputs/find_population_tx_implications/5.json index 98a09437b..07c83576c 100644 --- a/tests/expected_outputs/find_population_tx_implications/5.json +++ b/tests/expected_outputs/find_population_tx_implications/5.json @@ -1,19 +1,18 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "implications", "part": [ { - "name": "numerator", + "name": "denominator", "valueQuantity": { - "value": 14 + "value": 1116 } }, { - "name": "denominator", + "name": "numerator", "valueQuantity": { - "value": 1116 + "value": 14 } }, { @@ -74,5 +73,6 @@ } ] } - ] -} + ], + "resourceType": "Parameters" +} \ No newline at end of file diff --git a/tests/expected_outputs/find_study_metadata/1.json b/tests/expected_outputs/find_study_metadata/1.json index f7977898e..e39820ab0 100644 --- a/tests/expected_outputs/find_study_metadata/1.json +++ b/tests/expected_outputs/find_study_metadata/1.json @@ -1,66 +1,66 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "tests", "part": [ - { - "name": "testID", - "valueString": "ABC123-T1" - }, - { - "name": "testDate", - "valueString": "2020-09-20 00:00:00" - }, - { - "name": "specimenId", - "valueString": "ABC123-Sp1" - }, - { - "name": "genomicBuild", - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA14029-5", - "display": "GRCh37" - } - ] - } - }, { "name": "dnaChangeType", "valueCodeableConcept": { "coding": [ { - "system": "http://sequenceontology.org", - "code": "SO:0000667", - "display": "INS" + "code": "SO:0000159", + "display": "DEL", + "system": "http://sequenceontology.org" }, { - "system": "http://sequenceontology.org", - "code": "SO:1000036", - "display": "INV" + "code": "SO:0000667", + "display": "INS", + "system": "http://sequenceontology.org" }, { - "system": "http://sequenceontology.org", "code": "SO:0001019", - "display": "CNV" + "display": "CNV", + "system": "http://sequenceontology.org" }, { - "system": "http://sequenceontology.org", - "code": "SO:0000159", - "display": "DEL" + "code": "SO:0001019", + "display": "DUP", + "system": "http://sequenceontology.org" }, { - "system": "http://sequenceontology.org", - "code": "SO:0001019", - "display": "DUP" + "code": "SO:1000036", + "display": "INV", + "system": "http://sequenceontology.org" + } + ] + } + }, + { + "name": "genomicBuild", + "valueCodeableConcept": { + "coding": [ + { + "code": "LA14029-5", + "display": "GRCh37", + "system": "http://loinc.org" } ] } + }, + { + "name": "specimenId", + "valueString": "ABC123-Sp1" + }, + { + "name": "testDate", + "valueString": "2020-09-20 00:00:00" + }, + { + "name": "testID", + "valueString": "ABC123-T1" } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_study_metadata/2.json b/tests/expected_outputs/find_study_metadata/2.json index ee1326ed2..6c880d44e 100644 --- a/tests/expected_outputs/find_study_metadata/2.json +++ b/tests/expected_outputs/find_study_metadata/2.json @@ -1,133 +1,133 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "tests", "part": [ { - "name": "testID", - "valueString": "HCC1143-T1" - }, - { - "name": "testDate", - "valueString": "2020-02-03 00:00:00" - }, - { - "name": "specimenId", - "valueString": "HCC1143-Sp1" - }, - { - "name": "genomicBuild", + "name": "dnaChangeType", "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": " LA26806-2", - "display": "GRCh38" + "code": "SO:0000159", + "display": "DEL", + "system": "http://sequenceontology.org" + }, + { + "code": "SO:0000667", + "display": "INS", + "system": "http://sequenceontology.org" + }, + { + "code": "SO:0001019", + "display": "CNV", + "system": "http://sequenceontology.org" + }, + { + "code": "SO:0001019", + "display": "DUP", + "system": "http://sequenceontology.org" + }, + { + "code": "SO:1000036", + "display": "INV", + "system": "http://sequenceontology.org" } ] } }, { - "name": "dnaChangeType", + "name": "genomicBuild", "valueCodeableConcept": { "coding": [ { - "system": "http://sequenceontology.org", - "code": "SO:0001483", - "display": "SNV" - }, - { - "system": "http://sequenceontology.org", - "code": "SO:0002007", - "display": "MNV" - }, - { - "system": "http://sequenceontology.org", - "code": "SO:1000032", - "display": "delins" + "code": "LA14029-5", + "display": "GRCh37", + "system": "http://loinc.org" } ] } }, { "name": "regionStudied", - "valueString": "['NC_000007.14:55019016-55211628']" + "valueString": "['NC_000007.13:55086709-55279321']" }, { - "name": "uncallableRegions", - "valueString": "unknown" - } - ] - }, - { - "name": "tests", - "part": [ - { - "name": "testID", - "valueString": "HCC1143-T2" + "name": "specimenId", + "valueString": "HCC1143-Sp1" }, { "name": "testDate", "valueString": "2020-02-17 00:00:00" }, { - "name": "specimenId", - "valueString": "HCC1143-Sp1" + "name": "testID", + "valueString": "HCC1143-T2" }, { - "name": "genomicBuild", + "name": "uncallableRegions", + "valueString": "['NC_000007.13:55174000-55175000']" + } + ] + }, + { + "name": "tests", + "part": [ + { + "name": "dnaChangeType", "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA14029-5", - "display": "GRCh37" + "code": "SO:0001483", + "display": "SNV", + "system": "http://sequenceontology.org" + }, + { + "code": "SO:0002007", + "display": "MNV", + "system": "http://sequenceontology.org" + }, + { + "code": "SO:1000032", + "display": "delins", + "system": "http://sequenceontology.org" } ] } }, { - "name": "dnaChangeType", + "name": "genomicBuild", "valueCodeableConcept": { "coding": [ { - "system": "http://sequenceontology.org", - "code": "SO:0000667", - "display": "INS" - }, - { - "system": "http://sequenceontology.org", - "code": "SO:1000036", - "display": "INV" - }, - { - "system": "http://sequenceontology.org", - "code": "SO:0001019", - "display": "CNV" - }, - { - "system": "http://sequenceontology.org", - "code": "SO:0000159", - "display": "DEL" - }, - { - "system": "http://sequenceontology.org", - "code": "SO:0001019", - "display": "DUP" + "code": " LA26806-2", + "display": "GRCh38", + "system": "http://loinc.org" } ] } }, { "name": "regionStudied", - "valueString": "['NC_000007.13:55086709-55279321']" + "valueString": "['NC_000007.14:55019016-55211628']" + }, + { + "name": "specimenId", + "valueString": "HCC1143-Sp1" + }, + { + "name": "testDate", + "valueString": "2020-02-03 00:00:00" + }, + { + "name": "testID", + "valueString": "HCC1143-T1" }, { "name": "uncallableRegions", - "valueString": "['NC_000007.13:55174000-55175000']" + "valueString": "unknown" } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_study_metadata/3.json b/tests/expected_outputs/find_study_metadata/3.json index ee1326ed2..6c880d44e 100644 --- a/tests/expected_outputs/find_study_metadata/3.json +++ b/tests/expected_outputs/find_study_metadata/3.json @@ -1,133 +1,133 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "tests", "part": [ { - "name": "testID", - "valueString": "HCC1143-T1" - }, - { - "name": "testDate", - "valueString": "2020-02-03 00:00:00" - }, - { - "name": "specimenId", - "valueString": "HCC1143-Sp1" - }, - { - "name": "genomicBuild", + "name": "dnaChangeType", "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": " LA26806-2", - "display": "GRCh38" + "code": "SO:0000159", + "display": "DEL", + "system": "http://sequenceontology.org" + }, + { + "code": "SO:0000667", + "display": "INS", + "system": "http://sequenceontology.org" + }, + { + "code": "SO:0001019", + "display": "CNV", + "system": "http://sequenceontology.org" + }, + { + "code": "SO:0001019", + "display": "DUP", + "system": "http://sequenceontology.org" + }, + { + "code": "SO:1000036", + "display": "INV", + "system": "http://sequenceontology.org" } ] } }, { - "name": "dnaChangeType", + "name": "genomicBuild", "valueCodeableConcept": { "coding": [ { - "system": "http://sequenceontology.org", - "code": "SO:0001483", - "display": "SNV" - }, - { - "system": "http://sequenceontology.org", - "code": "SO:0002007", - "display": "MNV" - }, - { - "system": "http://sequenceontology.org", - "code": "SO:1000032", - "display": "delins" + "code": "LA14029-5", + "display": "GRCh37", + "system": "http://loinc.org" } ] } }, { "name": "regionStudied", - "valueString": "['NC_000007.14:55019016-55211628']" + "valueString": "['NC_000007.13:55086709-55279321']" }, { - "name": "uncallableRegions", - "valueString": "unknown" - } - ] - }, - { - "name": "tests", - "part": [ - { - "name": "testID", - "valueString": "HCC1143-T2" + "name": "specimenId", + "valueString": "HCC1143-Sp1" }, { "name": "testDate", "valueString": "2020-02-17 00:00:00" }, { - "name": "specimenId", - "valueString": "HCC1143-Sp1" + "name": "testID", + "valueString": "HCC1143-T2" }, { - "name": "genomicBuild", + "name": "uncallableRegions", + "valueString": "['NC_000007.13:55174000-55175000']" + } + ] + }, + { + "name": "tests", + "part": [ + { + "name": "dnaChangeType", "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA14029-5", - "display": "GRCh37" + "code": "SO:0001483", + "display": "SNV", + "system": "http://sequenceontology.org" + }, + { + "code": "SO:0002007", + "display": "MNV", + "system": "http://sequenceontology.org" + }, + { + "code": "SO:1000032", + "display": "delins", + "system": "http://sequenceontology.org" } ] } }, { - "name": "dnaChangeType", + "name": "genomicBuild", "valueCodeableConcept": { "coding": [ { - "system": "http://sequenceontology.org", - "code": "SO:0000667", - "display": "INS" - }, - { - "system": "http://sequenceontology.org", - "code": "SO:1000036", - "display": "INV" - }, - { - "system": "http://sequenceontology.org", - "code": "SO:0001019", - "display": "CNV" - }, - { - "system": "http://sequenceontology.org", - "code": "SO:0000159", - "display": "DEL" - }, - { - "system": "http://sequenceontology.org", - "code": "SO:0001019", - "display": "DUP" + "code": " LA26806-2", + "display": "GRCh38", + "system": "http://loinc.org" } ] } }, { "name": "regionStudied", - "valueString": "['NC_000007.13:55086709-55279321']" + "valueString": "['NC_000007.14:55019016-55211628']" + }, + { + "name": "specimenId", + "valueString": "HCC1143-Sp1" + }, + { + "name": "testDate", + "valueString": "2020-02-03 00:00:00" + }, + { + "name": "testID", + "valueString": "HCC1143-T1" }, { "name": "uncallableRegions", - "valueString": "['NC_000007.13:55174000-55175000']" + "valueString": "unknown" } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_study_metadata/4.json b/tests/expected_outputs/find_study_metadata/4.json index cc436b762..4e2d68d2e 100644 --- a/tests/expected_outputs/find_study_metadata/4.json +++ b/tests/expected_outputs/find_study_metadata/4.json @@ -1,133 +1,133 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "tests", "part": [ { - "name": "testID", - "valueString": "HCC1143-T1" - }, - { - "name": "testDate", - "valueString": "2020-02-03 00:00:00" - }, - { - "name": "specimenId", - "valueString": "HCC1143-Sp1" - }, - { - "name": "genomicBuild", + "name": "dnaChangeType", "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": " LA26806-2", - "display": "GRCh38" + "code": "SO:0000159", + "display": "DEL", + "system": "http://sequenceontology.org" + }, + { + "code": "SO:0000667", + "display": "INS", + "system": "http://sequenceontology.org" + }, + { + "code": "SO:0001019", + "display": "CNV", + "system": "http://sequenceontology.org" + }, + { + "code": "SO:0001019", + "display": "DUP", + "system": "http://sequenceontology.org" + }, + { + "code": "SO:1000036", + "display": "INV", + "system": "http://sequenceontology.org" } ] } }, { - "name": "dnaChangeType", + "name": "genomicBuild", "valueCodeableConcept": { "coding": [ { - "system": "http://sequenceontology.org", - "code": "SO:0001483", - "display": "SNV" - }, - { - "system": "http://sequenceontology.org", - "code": "SO:0002007", - "display": "MNV" - }, - { - "system": "http://sequenceontology.org", - "code": "SO:1000032", - "display": "delins" + "code": "LA14029-5", + "display": "GRCh37", + "system": "http://loinc.org" } ] } }, { "name": "regionStudied", - "valueString": "['NC_000006.12:26091075-26091079']" + "valueString": "['NC_000006.11:26091303-26091307']" }, { - "name": "uncallableRegions", - "valueString": "unknown" - } - ] - }, - { - "name": "tests", - "part": [ - { - "name": "testID", - "valueString": "HCC1143-T2" + "name": "specimenId", + "valueString": "HCC1143-Sp1" }, { "name": "testDate", "valueString": "2020-02-17 00:00:00" }, { - "name": "specimenId", - "valueString": "HCC1143-Sp1" + "name": "testID", + "valueString": "HCC1143-T2" }, { - "name": "genomicBuild", + "name": "uncallableRegions", + "valueString": "[]" + } + ] + }, + { + "name": "tests", + "part": [ + { + "name": "dnaChangeType", "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA14029-5", - "display": "GRCh37" + "code": "SO:0001483", + "display": "SNV", + "system": "http://sequenceontology.org" + }, + { + "code": "SO:0002007", + "display": "MNV", + "system": "http://sequenceontology.org" + }, + { + "code": "SO:1000032", + "display": "delins", + "system": "http://sequenceontology.org" } ] } }, { - "name": "dnaChangeType", + "name": "genomicBuild", "valueCodeableConcept": { "coding": [ { - "system": "http://sequenceontology.org", - "code": "SO:0000667", - "display": "INS" - }, - { - "system": "http://sequenceontology.org", - "code": "SO:1000036", - "display": "INV" - }, - { - "system": "http://sequenceontology.org", - "code": "SO:0001019", - "display": "CNV" - }, - { - "system": "http://sequenceontology.org", - "code": "SO:0000159", - "display": "DEL" - }, - { - "system": "http://sequenceontology.org", - "code": "SO:0001019", - "display": "DUP" + "code": " LA26806-2", + "display": "GRCh38", + "system": "http://loinc.org" } ] } }, { "name": "regionStudied", - "valueString": "['NC_000006.11:26091303-26091307']" + "valueString": "['NC_000006.12:26091075-26091079']" + }, + { + "name": "specimenId", + "valueString": "HCC1143-Sp1" + }, + { + "name": "testDate", + "valueString": "2020-02-03 00:00:00" + }, + { + "name": "testID", + "valueString": "HCC1143-T1" }, { "name": "uncallableRegions", - "valueString": "[]" + "valueString": "unknown" } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_dx_implications/1.json b/tests/expected_outputs/find_subject_dx_implications/1.json index 4cae06f76..a9b02fc6e 100644 --- a/tests/expected_outputs/find_subject_dx_implications/1.json +++ b/tests/expected_outputs/find_subject_dx_implications/1.json @@ -1,23 +1,14 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "implication", "resource": { - "resourceType": "Observation", - "id": "dv-62fab6f25932091e78c68d2f", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -25,36 +16,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/huC30902" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-aad8639bd558470a9ca8612eae011065" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA26333-7", - "display": "Uncertain significance" + "display": "Uncertain significance", + "system": "http://loinc.org" } ] } @@ -63,18 +46,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C1708353", - "display": "Hereditary pheochromocytoma-paraganglioma" + "display": "Hereditary pheochromocytoma-paraganglioma", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -83,9 +66,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -94,6 +77,12 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-aad8639bd558470a9ca8612eae011065" + } + ], + "id": "dv-62fab6f25932091e78c68d2f", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -103,26 +92,28 @@ "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", "value": "SCV001252233.1" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-aad8639bd558470a9ca8612eae011065", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/huC30902" + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -130,21 +121,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/huC30902" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -153,18 +132,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -173,17 +152,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000001.10" + "code": "NC_000001.10", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -192,18 +171,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -212,101 +191,122 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "C" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000001.10:161333381:C:T", - "display": "NC_000001.10:161333381:C:T" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000001.10:161333381:C:T", + "display": "NC_000001.10:161333381:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueRange": { + "low": { + "value": 161333381 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 161333381 - } } } - ] + ], + "id": "dv-aad8639bd558470a9ca8612eae011065", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/huC30902" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_dx_implications/2.json b/tests/expected_outputs/find_subject_dx_implications/2.json index be84ca30a..d41f13958 100644 --- a/tests/expected_outputs/find_subject_dx_implications/2.json +++ b/tests/expected_outputs/find_subject_dx_implications/2.json @@ -1,23 +1,14 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "implication", "resource": { - "resourceType": "Observation", - "id": "dv-62fab6475932091e78bff0a1", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -25,36 +16,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/huC30902" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-d9c5ad61266c4f3c90e44199a8864662" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA26333-7", + "display": "Uncertain significance", + "system": "http://loinc.org" } ] } @@ -63,18 +46,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C1708353", - "display": "Hereditary pheochromocytoma-paraganglioma" + "display": "Hereditary pheochromocytoma-paraganglioma", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -83,9 +66,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -94,35 +77,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-aad8639bd558470a9ca8612eae011065" + } + ], + "id": "dv-62fab6f25932091e78c68d2f", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "44641" + "value": "873683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000351450.3" + "value": "SCV001252233.1" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-d9c5ad61266c4f3c90e44199a8864662", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/huC30902" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -130,21 +121,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/huC30902" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -153,18 +131,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -173,17 +151,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000001.10" + "code": "C1708353", + "display": "Hereditary pheochromocytoma-paraganglioma", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -192,18 +171,84 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-d9c5ad61266c4f3c90e44199a8864662" + } + ], + "id": "dv-62fab6475932091e78bff0a1", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "44641" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000351450.3" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/huC30902" + } + } + }, + { + "name": "variant", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" + } + ] + }, + "component": [ + { + "code": { + "coding": [ + { + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -212,18 +257,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000001.10:17380496:G:T", - "display": "NC_000001.10:17380496:G:T" + "code": "NC_000001.10", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -232,26 +276,29 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -261,9 +308,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, @@ -273,18 +320,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000001.10:17380496:G:T", + "display": "NC_000001.10:17380496:G:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -293,9 +340,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, @@ -309,143 +356,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.973659, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6f25932091e78c68d2f", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 } - ] - }, - "subject": { - "reference": "Patient/huC30902" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-aad8639bd558470a9ca8612eae011065" - } - ], - "component": [ + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA26333-7", - "display": "Uncertain significance" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.973659 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C1708353", - "display": "Hereditary pheochromocytoma-paraganglioma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "873683" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001252233.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-aad8639bd558470a9ca8612eae011065", + "id": "dv-d9c5ad61266c4f3c90e44199a8864662", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/huC30902" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -453,21 +444,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/huC30902" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -476,18 +455,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -496,17 +475,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000001.10" + "code": "NC_000001.10", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -515,18 +494,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -535,101 +514,122 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "C" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000001.10:161333381:C:T", - "display": "NC_000001.10:161333381:C:T" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000001.10:161333381:C:T", + "display": "NC_000001.10:161333381:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueRange": { + "low": { + "value": 161333381 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 161333381 - } } } - ] + ], + "id": "dv-aad8639bd558470a9ca8612eae011065", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/huC30902" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_dx_implications/3.json b/tests/expected_outputs/find_subject_dx_implications/3.json index 15ee12c4b..4fb4edef8 100644 --- a/tests/expected_outputs/find_subject_dx_implications/3.json +++ b/tests/expected_outputs/find_subject_dx_implications/3.json @@ -1,23 +1,14 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "implication", "resource": { - "resourceType": "Observation", - "id": "dv-62fab6ab5932091e78c3cfb0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -25,36 +16,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-dd6a5ae0dbc24360aea5a7c161101a68" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA26333-7", - "display": "Uncertain significance" + "display": "Uncertain significance", + "system": "http://loinc.org" } ] } @@ -63,18 +46,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C4552100", - "display": "Lynch syndrome" + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -83,9 +66,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -94,6 +77,12 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-dd6a5ae0dbc24360aea5a7c161101a68" + } + ], + "id": "dv-62fab6ab5932091e78c3cfb0", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -103,26 +92,28 @@ "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", "value": "SCV000430916.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-dd6a5ae0dbc24360aea5a7c161101a68", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -130,21 +121,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -153,18 +131,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA26333-7", + "display": "Uncertain significance", + "system": "http://loinc.org" } ] } @@ -173,17 +151,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - 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+ "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "TAA" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C0020445", + "display": "Familial hypercholesterolemia", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -293,38 +276,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 47414419 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6665932091e78c11fa3", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-1692d4f52d4944a391a1e1e57347d8eb" + } + ], + "id": "dv-62fab66e5932091e78c17715", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "128422" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV002524050.1" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -332,36 +331,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": 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"system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-1692d4f52d4944a391a1e1e57347d8eb" + } + ], + "id": "dv-62fab66e5932091e78c17717", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90368" + "value": "128422" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106876.2" + "value": "SCV000902527.1" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e1932783d03241559c7627fcde3fbec2", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -437,21 +436,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -460,18 +446,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -480,17 +466,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "C0020445", + "display": "Familial hypercholesterolemia", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -499,99 +486,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37016099:C:T", - "display": "NC_000003.12:37016099:C:T" - } - ] - } + "reference": "Observation/dv-37304b7e844c41258d4a25a6dffada5b" + } + ], + "id": "dv-62fab69e5932091e78c3549d", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "252262" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001717062.2" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "C" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C0020445", + "display": "Familial hypercholesterolemia", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -600,38 +591,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 37016099 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6665932091e78c126e8", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-5c81355782d446179e37701af154f50b" + } + ], + "id": "dv-62fab6305932091e78bf264e", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "2878" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000690958.2" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -639,36 +646,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-4bde3f4b60a843a88d84e9974aa86fa7" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -677,18 +676,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0020445", + "display": "Familial hypercholesterolemia", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -697,46 +696,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-6f1550b878b740c29dae310d745dbc76" + } + ], + "id": "dv-62fab6a85932091e78c3bb46", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90924" + "value": "328058" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107454.2" + "value": "SCV001717063.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-4bde3f4b60a843a88d84e9974aa86fa7", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -744,21 +751,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -767,18 +761,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -787,17 +781,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "C0020445", + "display": "Familial hypercholesterolemia", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -806,38 +801,83 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-719286980a454cc792902098a0122614" + } + ], + "id": "dv-62fab66e5932091e78c176b0", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "128416" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000902556.1" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" + } + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47476887:G:C", - "display": "NC_000002.12:47476887:G:C" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -846,59 +886,123 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "C0020445", + "display": "Familial hypercholesterolemia", + "system": "https://www.ncbi.nlm.nih.gov/medgen" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "derivedFrom": [ + { + "reference": 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"Genomic Alt allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueCodeableConcept": { + "coding": [ + { + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" + } + ] + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C0020445", + "display": "Familial hypercholesterolemia", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -907,38 +1011,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 47476887 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6ab5932091e78c3cfb3", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-b5fde7b61b29434bb495e2bca5859063" + } + ], + "id": "dv-62fab69e5932091e78c34f8c", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "251936" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001727625.2" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -946,36 +1066,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-dd6a5ae0dbc24360aea5a7c161101a68" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA26333-7", - "display": "Uncertain significance" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -984,18 +1096,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0020445", + "display": "Familial hypercholesterolemia", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1004,9 +1116,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -1015,35 +1127,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-b96b0bdcbc3a4a68913378136736b773" + } + ], + "id": "dv-62fab66e5932091e78c17733", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "336427" + "value": "128425" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000430917.2" + "value": "SCV000902523.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf71d5", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1051,36 +1171,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-38f8d84905ff4a5e9547b1e339f3ce02" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -1089,18 +1201,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0020445", + "display": "Familial hypercholesterolemia", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1109,46 +1221,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-d675ed9e0e514a478542b503a5250ab3" + } + ], + "id": "dv-62fab66e5932091e78c176c8", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36685" + "value": "128418" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000053031.2" + "value": "SCV000902521.1" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-38f8d84905ff4a5e9547b1e339f3ce02", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1156,21 +1276,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -1179,18 +1286,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -1199,17 +1306,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "code": "C0020445", + "display": "Familial hypercholesterolemia", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1218,38 +1326,83 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-f2bfcff0b23a4c15a74aaeaef5faec4f" + } + ], + "id": "dv-62fab7095932091e78c75e4d", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "1168905" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV002053227.1" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" + } + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:5987356:G:A", - "display": "NC_000007.14:5987356:G:A" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -1258,59 +1411,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "C0020445", + "display": "Familial hypercholesterolemia", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-f2d0de4c461c487fa0d7b2b0a9034361" + } + ], + "id": "dv-62fab68a5932091e78c28ec6", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "200916" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001729839.2" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" + } + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -1319,54 +1516,74 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 5987356 - } + "valueCodeableConcept": { + "coding": [ + { + "code": "C0020445", + "display": "Familial hypercholesterolemia", + "system": "https://www.ncbi.nlm.nih.gov/medgen" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.387786, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "no assertion criteria provided" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf7251", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-37304b7e844c41258d4a25a6dffada5b" + } + ], + "id": "dv-62fab69e5932091e78c3549c", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "252262" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001461329.1" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1374,36 +1591,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-4435221b91444669b3f6237f6b6fa954" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -1412,18 +1621,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0020445", + "display": "Familial hypercholesterolemia", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1432,46 +1641,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f2d0de4c461c487fa0d7b2b0a9034361" + } + ], + "id": "dv-62fab68a5932091e78c28ebb", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36692" + "value": "200916" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108377.2" + "value": "SCV001460277.1" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-4435221b91444669b3f6237f6b6fa954", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1479,21 +1696,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -1502,18 +1706,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -1522,17 +1726,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + 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"display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" + } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-57863b6706444b2e9fabc5d5808df40a" + } + ], + "id": "dv-62fab6725932091e78c1a029", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "137691" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV002505088.1" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" + } + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -1642,54 +1936,74 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 5999090 - } + "valueCodeableConcept": { + "coding": [ + { + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.368213, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf6fcc", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-87f77277c4c84151bb54754435b23d8c" + } + ], + "id": "dv-62fab68e5932091e78c2b13d", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "209600" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001000937.4" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1697,36 +2011,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b8cc4e2fbe604134979c80e1aa8c4cee" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -1735,18 +2041,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1755,46 +2061,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-99d2b1819c554636b70c366c3f79f914" + } + ], + "id": "dv-62fab66c5932091e78c15b7b", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36594" + "value": "125991" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108147.2" + "value": "SCV001719551.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-b8cc4e2fbe604134979c80e1aa8c4cee", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1802,21 +2116,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -1825,18 +2126,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -1845,17 +2146,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1864,99 +2166,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47806411:C:G", - "display": "NC_000002.12:47806411:C:G" - } - ] - } + "reference": "Observation/dv-c05bb5adae894ebc865a6808c7685992" + } + ], + "id": "dv-62fab6705932091e78c186e3", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "133738" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV002025816.2" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "C" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1965,54 +2271,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 47806411 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-c05bb5adae894ebc865a6808c7685992" + } + ], + "id": "dv-62fab6705932091e78c186e7", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "133738" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.733985, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001000149.4" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66e5932091e78c17715", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2020,36 +2326,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-1692d4f52d4944a391a1e1e57347d8eb" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -2058,18 +2356,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -2078,9 +2376,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -2089,35 +2387,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c7c0803976fd4ab881f1588c713419ff" + } + ], + "id": "dv-62fab66f5932091e78c17cb2", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "128422" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002524050.1" + "value": "SCV002026104.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-1692d4f52d4944a391a1e1e57347d8eb", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2125,21 +2431,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2148,18 +2441,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -2168,17 +2461,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -2187,99 +2481,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:21041027:G:A", 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"http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "G" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "A" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -2288,54 +2586,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 21041027 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-c7c0803976fd4ab881f1588c713419ff" + } + ], + "id": "dv-62fab66f5932091e78c17cc2", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132779" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.25802, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000494326.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6645932091e78c11178", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2343,36 +2641,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-234ee4ca3da04ab39f5ebfed027792dd" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -2381,18 +2671,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": 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"Observation", - "id": "dv-234ee4ca3da04ab39f5ebfed027792dd", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2448,21 +2746,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2471,18 +2756,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -2491,17 +2776,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -2510,99 +2796,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47791516:T:C", - "display": "NC_000002.12:47791516:T:C" - } - ] - } + "reference": "Observation/dv-d47c74da1d8340e3976b600eedc794ac" + } + ], + "id": "dv-62fab66f5932091e78c17cd7", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000635514.5" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "T" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -2611,38 +2901,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 47791516 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6645932091e78c11177", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-d47c74da1d8340e3976b600eedc794ac" + } + ], + "id": "dv-62fab66f5932091e78c17ce1", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000494339.1" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2650,36 +2956,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-1aa0fdfa74344f23b55e811414e4dcdf" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -2688,18 +2986,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -2708,46 +3006,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-edfe8714ceaf4687910f600e46f6806e" + } + ], + "id": "dv-62fab66c5932091e78c15bf3", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89521" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108207.2" + "value": "SCV001000460.4" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-1aa0fdfa74344f23b55e811414e4dcdf", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2755,21 +3061,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2778,18 +3071,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -2798,17 +3091,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -2817,99 +3111,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47792345:T:C", - "display": "NC_000002.12:47792345:T:C" - } - ] - } + "reference": "Observation/dv-edfe8714ceaf4687910f600e46f6806e" + } + ], + "id": "dv-62fab66c5932091e78c15c00", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000494320.1" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "T" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -2918,38 +3216,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 47792345 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15c00", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-edfe8714ceaf4687910f600e46f6806e" + } + ], + "id": "dv-62fab66c5932091e78c15c01", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV002026093.2" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2957,36 +3271,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-edfe8714ceaf4687910f600e46f6806e" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -2995,18 +3301,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -3015,9 +3321,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -3026,35 +3332,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-210349083123421e9899d9f21af3ef71" + } + ], + "id": "dv-62fab6395932091e78bf6bfe", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "36564" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000494320.1" + "value": "SCV000052904.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-edfe8714ceaf4687910f600e46f6806e", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3062,21 +3376,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -3085,18 +3386,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -3105,17 +3406,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.11" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] 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"implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" + } + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.11:32338161:T:C", - "display": "NC_000013.11:32338161:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - 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"LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32338161 - } - } + "reference": "Observation/dv-4435221b91444669b3f6237f6b6fa954" + } + ], + "id": "dv-62fab63a5932091e78bf7252", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "36692" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000053038.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6395932091e78bf6bfd", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3280,36 +3586,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-210349083123421e9899d9f21af3ef71" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -3318,18 +3616,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C4552100", - "display": "Lynch syndrome" + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -3338,46 +3636,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-5940367f4ed843f59a836f0cdce1dafe" + } + ], + "id": "dv-62fab63a5932091e78bf725d", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36564" + "value": "36693" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107047.2" + "value": "SCV000053039.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-210349083123421e9899d9f21af3ef71", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3385,21 +3691,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -3408,18 +3701,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -3428,17 +3721,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -3447,99 +3741,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47429661:G:A", - "display": "NC_000002.12:47429661:G:A" - } - ] - } + "reference": "Observation/dv-70b3a31ae2224e559d8be65a11a9eddb" + } + ], + "id": "dv-62fab63a5932091e78bf6f98", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "36587" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000052932.2" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "G" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "A" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -3548,38 +3846,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 47429661 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab68e5932091e78c2b13d", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-aab391f842a14a79865639fc25b95ff9" + } + ], + "id": "dv-62fab63a5932091e78bf6fdb", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "36597" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000052942.2" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3587,36 +3901,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-87f77277c4c84151bb54754435b23d8c" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -3625,18 +3931,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -3645,9 +3951,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -3656,35 +3962,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-b8cc4e2fbe604134979c80e1aa8c4cee" + } + ], + "id": "dv-62fab63a5932091e78bf6fd4", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "209600" + "value": "36594" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001000937.4" + "value": "SCV000052939.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-87f77277c4c84151bb54754435b23d8c", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3692,21 +4006,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -3715,18 +4016,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -3735,17 +4036,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.11" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -3754,99 +4056,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.11:32315654:A:G", - "display": "NC_000013.11:32315654:A:G" - } - ] - } + "reference": "Observation/dv-db2c78d7a2d84f6a9a8927fb296cb567" + } + ], + "id": "dv-62fab63a5932091e78bf6f6e", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "36584" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000052928.2" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -3855,38 +4161,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 32315654 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-e28737e34fd843fbbe1717b56b96d1f8" + } + ], "id": "dv-62fab6905932091e78c2c798", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "218461" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000257705.2" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3894,36 +4216,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e28737e34fd843fbbe1717b56b96d1f8" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -3932,18 +4246,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C4552100", - "display": "Lynch syndrome" + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -3952,9 +4266,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -3963,6 +4277,12 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e28737e34fd843fbbe1717b56b96d1f8" + } + ], + "id": "dv-62fab6905932091e78c2c79a", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -3970,28 +4290,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000257705.2" + "value": "SCV000257707.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e28737e34fd843fbbe1717b56b96d1f8", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3999,21 +4321,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -4022,18 +4331,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -4042,17 +4351,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -4061,99 +4371,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "no assertion criteria provided" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-38f8d84905ff4a5e9547b1e339f3ce02" + } + ], + "id": "dv-62fab63a5932091e78bf71d5", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "36685" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:5997426:AAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA", - "display": "NC_000007.14:5997426:AAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA" - } - ] - } - }, + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000053031.2" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "GA" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -4162,54 +4476,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 5997425 - } + "valueCodeableConcept": { + "text": "reviewed by expert panel" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-0c3e9547181e4b789c13b04121a9ced8" + } + ], + "id": "dv-62fab6655932091e78c1145b", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "89611" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.430816, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000106069.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf6f98", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4217,36 +4531,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-70b3a31ae2224e559d8be65a11a9eddb" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -4255,18 +4561,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C4552100", - "display": "Lynch syndrome" + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -4275,46 +4581,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-1aa0fdfa74344f23b55e811414e4dcdf" + } + ], + "id": "dv-62fab6645932091e78c11177", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36587" + "value": "89521" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000052932.2" + "value": "SCV000108207.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-70b3a31ae2224e559d8be65a11a9eddb", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4322,21 +4636,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -4345,18 +4646,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -4365,17 +4666,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -4384,155 +4686,159 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "reviewed by expert panel" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-210349083123421e9899d9f21af3ef71" + } + ], + "id": "dv-62fab6395932091e78bf6bfd", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "36564" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000107047.2" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" + } + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47790941:A:G", - "display": "NC_000002.12:47790941:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "reviewed by expert panel" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 47790941 - } - } + "reference": "Observation/dv-234ee4ca3da04ab39f5ebfed027792dd" + } + ], + "id": "dv-62fab6645932091e78c11178", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "89525" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.134727, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000108211.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf7252", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4540,36 +4846,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-4435221b91444669b3f6237f6b6fa954" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -4578,18 +4876,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C4552100", - "display": "Lynch syndrome" + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -4598,46 +4896,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-2439d4f778564bdd88dc95b2864fac18" + } + ], + "id": "dv-62fab6645932091e78c10df7", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36692" + "value": "89345" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000053038.2" + "value": "SCV000108022.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6645932091e78c11181", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4645,36 +4951,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-49c6c5a200fb42fba2c02268d74d00a3" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -4683,18 +4981,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C4552100", - "display": "Lynch syndrome" + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -4703,9 +5001,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -4714,35 +5012,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-324e0f6400104fc4846edb4fa8d66008" + } + ], + "id": "dv-62fab6655932091e78c11493", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89526" + "value": "89625" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108213.2" + "value": "SCV000106085.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-49c6c5a200fb42fba2c02268d74d00a3", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4750,21 +5056,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -4773,18 +5066,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -4793,17 +5086,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -4812,99 +5106,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "reviewed by expert panel" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47791174:T:A", - "display": "NC_000002.12:47791174:T:A" - } - ] - } + "reference": "Observation/dv-32bc0d97fc48469c8f3bf615dc186530" + } + ], + "id": "dv-62fab6645932091e78c10fbb", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "89432" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000108113.2" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "T" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "A" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -4913,38 +5211,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 47791174 - } + "valueCodeableConcept": { + "text": "reviewed by expert panel" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6655932091e78c1145b", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-37cd8d0c069d43cca4761374a718b6e8" + } + ], + "id": "dv-62fab6645932091e78c111bb", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "89543" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000108232.2" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4952,36 +5266,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0c3e9547181e4b789c13b04121a9ced8" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -4990,18 +5296,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C4552100", - "display": "Lynch syndrome" + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -5010,9 +5316,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -5021,35 +5327,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-38f8d84905ff4a5e9547b1e339f3ce02" + } + ], + "id": "dv-62fab63a5932091e78bf71dc", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89611" + "value": "36685" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106069.2" + "value": "SCV000108294.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0c3e9547181e4b789c13b04121a9ced8", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5057,21 +5371,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -5080,37 +5381,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -5119,18 +5401,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -5139,119 +5421,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37021467:G:T", - "display": "NC_000003.12:37021467:G:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "text": "reviewed by expert panel" } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, + "reference": "Observation/dv-396515d9058748f2a3ce8d4e5149620b" + } + ], + "id": "dv-62fab6655932091e78c11a58", + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "90024" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 37021467 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000106504.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10b9e", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5259,36 +5476,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-525568db5bbb42e79c7b9c4b5d27fd28" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -5297,18 +5506,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C4552100", - "display": "Lynch syndrome" + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -5317,9 +5526,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -5328,35 +5537,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-3b3666df092d4e808a0d597a56a5022b" + } + ], + "id": "dv-62fab6645932091e78c10f6f", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89301" + "value": "89411" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107977.2" + "value": "SCV000108091.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-525568db5bbb42e79c7b9c4b5d27fd28", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5364,21 +5581,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -5387,18 +5591,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -5407,17 +5611,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -5426,99 +5631,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "reviewed by expert panel" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47790890:A:G", - "display": "NC_000002.12:47790890:A:G" - } - ] - } + "reference": "Observation/dv-437c728d910a46189036896c9a3fe97f" + } + ], + "id": "dv-62fab6395932091e78bf6afa", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "36542" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000106295.2" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -5527,54 +5736,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 47790890 - } + "valueCodeableConcept": { + "text": "reviewed by expert panel" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-4435221b91444669b3f6237f6b6fa954" + } + ], + "id": "dv-62fab63a5932091e78bf7251", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "36692" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.0372618, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000108377.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6665932091e78c1245b", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5582,36 +5791,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-ddbfcfdb118b4385a9dad7e38d9b6da5" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -5620,18 +5821,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C4552100", - "display": "Lynch syndrome" + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -5640,9 +5841,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -5651,35 +5852,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-49a4913593454c339fb981bd5144d9a6" + } + ], + "id": "dv-62fab6645932091e78c10b95", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90687" + "value": "89295" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107200.2" + "value": "SCV000107970.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-ddbfcfdb118b4385a9dad7e38d9b6da5", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5687,21 +5896,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -5710,18 +5906,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -5730,17 +5926,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -5749,38 +5946,83 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "reviewed by expert panel" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-49c6c5a200fb42fba2c02268d74d00a3" + } + ], + "id": "dv-62fab6645932091e78c11181", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "89526" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000108213.2" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" + } + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47465141:C:T", - "display": "NC_000002.12:47465141:C:T" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -5789,99 +6031,74 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "reviewed by expert panel" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-4bde3f4b60a843a88d84e9974aa86fa7" + } + ], + "id": "dv-62fab6665932091e78c126e8", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "90924" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 47465141 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000107454.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab68a5932091e78c28ebb", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5889,36 +6106,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f2d0de4c461c487fa0d7b2b0a9034361" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -5927,18 +6136,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -5947,46 +6156,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "reviewed by expert panel" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-4e13aba739b94934be7f63b77b87abf0" + } + ], + "id": "dv-62fab6665932091e78c12377", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "200916" + "value": "90609" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001460277.1" + "value": "SCV000107126.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f2d0de4c461c487fa0d7b2b0a9034361", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5994,21 +6211,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -6017,37 +6221,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.10" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -6056,18 +6241,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -6076,135 +6261,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.10:11113588:A:G", - "display": "NC_000019.10:11113588:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "text": "reviewed by expert panel" } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, + "reference": "Observation/dv-5071403516aa4a17871949bf246b8b5d" + } + ], + "id": "dv-62fab6435932091e78bfc9ac", + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11113588 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "42471" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.632026, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000108065.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10b9a", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6212,36 +6316,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-d83d284e564e4106a409fcd7bb222eb9" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -6250,18 +6346,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C4552100", - "display": "Lynch syndrome" + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -6270,9 +6366,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -6281,35 +6377,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-525568db5bbb42e79c7b9c4b5d27fd28" + } + ], + "id": "dv-62fab6645932091e78c10b9e", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89296" + "value": "89301" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107958.2" + "value": "SCV000107977.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-d83d284e564e4106a409fcd7bb222eb9", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6317,21 +6421,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -6340,18 +6431,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -6360,17 +6451,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -6379,99 +6471,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "reviewed by expert panel" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47785959:A:G", - "display": "NC_000002.12:47785959:A:G" - } - ] - } + "reference": "Observation/dv-5940367f4ed843f59a836f0cdce1dafe" + } + ], + "id": "dv-62fab63a5932091e78bf7276", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "36693" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000108381.2" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -6480,38 +6576,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 47785959 - } + "valueCodeableConcept": { + "text": "reviewed by expert panel" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6645932091e78c111bb", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-6b10bc016d794b2d891a2da2b7b49512" + } + ], + "id": "dv-62fab6645932091e78c10b9c", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "89300" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000107976.2" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6519,36 +6631,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-37cd8d0c069d43cca4761374a718b6e8" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -6557,18 +6661,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C4552100", - "display": "Lynch syndrome" + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -6577,9 +6681,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -6588,35 +6692,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-70b3a31ae2224e559d8be65a11a9eddb" + } + ], + "id": "dv-62fab63a5932091e78bf6f9a", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89543" + "value": "36587" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108232.2" + "value": "SCV000107992.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-37cd8d0c069d43cca4761374a718b6e8", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6624,21 +6736,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -6647,18 +6746,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -6667,17 +6766,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -6686,99 +6786,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "reviewed by expert panel" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-7dcdefbf50b7446eb461e5d998247478" + } + ], + "id": "dv-62fab6665932091e78c12386", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "90599" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47798554:C:T", - "display": "NC_000002.12:47798554:C:T" - } - ] - } - }, + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000107117.2" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "C" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -6787,38 +6891,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 47798554 - } + "valueCodeableConcept": { + "text": "reviewed by expert panel" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66e5932091e78c176c8", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-8154922662b44a9aa5260207fea8d5b6" + } + ], + "id": "dv-62fab6655932091e78c11355", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "89544" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000108233.2" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6826,36 +6946,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-d675ed9e0e514a478542b503a5250ab3" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -6864,18 +6976,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -6884,46 +6996,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-86d0233b22f3488197627b36c7594a73" + } + ], + "id": "dv-62fab6655932091e78c11695", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "128418" + "value": "89830" }, { "system": 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"reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -6954,18 +7061,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -6974,17 +7081,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": 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+ } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "C" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -7094,54 +7206,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 21002408 - } + "valueCodeableConcept": { + "text": "reviewed by expert panel" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-983532b4ef8b4928978bfaeba42af3db" + } + ], + "id": "dv-62fab6655932091e78c119bb", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "89983" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.704884, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000106463.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c3549d", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7149,36 +7261,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-37304b7e844c41258d4a25a6dffada5b" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -7187,18 +7291,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -7207,46 +7311,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-994f4ecf114a4bbb92bdb40776afc9b3" + } + ], + "id": "dv-62fab6665932091e78c11f9b", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "90366" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001717062.2" + "value": "SCV000106871.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-37304b7e844c41258d4a25a6dffada5b", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7254,21 +7366,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -7277,18 +7376,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -7297,17 +7396,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.10" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -7316,99 +7416,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "reviewed by expert panel" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.10:11123264:A:G", - "display": "NC_000019.10:11123264:A:G" - } - ] - } + "reference": "Observation/dv-a71417cfb7164f2090e77f29a9ead21a" + } + ], + "id": "dv-62fab6645932091e78c10fb4", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "89429" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000108111.2" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -7417,54 +7521,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 11123264 - } + "valueCodeableConcept": { + "text": "reviewed by expert panel" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-aa7bc4cb064c41b8939860b917dde5af" + } + ], + "id": "dv-62fab6655932091e78c11bb9", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "90146" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.781146, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000106634.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf71dc", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7472,36 +7576,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-38f8d84905ff4a5e9547b1e339f3ce02" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -7510,18 +7606,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C4552100", - "display": "Lynch syndrome" + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -7530,9 +7626,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -7541,35 +7637,43 @@ } } ], - "identifier": [ + "derivedFrom": [ { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36685" + "reference": "Observation/dv-aab391f842a14a79865639fc25b95ff9" + } + ], + "id": "dv-62fab63a5932091e78bf6fe4", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "36597" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108294.2" + "value": "SCV000108224.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10b9c", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7577,36 +7681,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-6b10bc016d794b2d891a2da2b7b49512" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -7615,18 +7711,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C4552100", - "display": "Lynch syndrome" + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -7635,9 +7731,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -7646,35 +7742,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-acb6861a2ae345cdae082be1563a4a66" + } + ], + "id": "dv-62fab6665932091e78c1262d", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89300" + "value": "90846" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107976.2" + "value": "SCV000107374.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-6b10bc016d794b2d891a2da2b7b49512", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7682,21 +7786,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -7705,37 +7796,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -7744,18 +7816,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -7764,119 +7836,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47789756:G:T", - "display": "NC_000002.12:47789756:G:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "text": "reviewed by expert panel" } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, + "reference": "Observation/dv-b8cc4e2fbe604134979c80e1aa8c4cee" + } + ], + "id": "dv-62fab63a5932091e78bf6fcc", + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "36594" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 47789756 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000108147.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb46", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7884,36 +7891,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-6f1550b878b740c29dae310d745dbc76" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -7922,18 +7921,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -7942,46 +7941,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-d35a9e4b945a443abf237057131c03e5" + } + ], + "id": "dv-62fab6675932091e78c13034", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328058" + "value": "91356" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001717063.2" + "value": "SCV000108367.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-6f1550b878b740c29dae310d745dbc76", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7989,21 +7996,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -8012,18 +8006,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -8032,17 +8026,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.10" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -8051,38 +8046,83 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "reviewed by expert panel" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-d83d284e564e4106a409fcd7bb222eb9" + } + ], + "id": "dv-62fab6645932091e78c10b9a", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "89296" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000107958.2" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" + } + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.10:11131630:G:C", - "display": "NC_000019.10:11131630:G:C" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -8091,59 +8131,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueCodeableConcept": { + "text": "reviewed by expert panel" + } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-db238eae873046a1bd607a546dc9381e" + } + ], + "id": "dv-62fab6645932091e78c10f67", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "89410" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000108090.2" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" + } + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -8152,54 +8236,74 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 11131630 - } + "valueCodeableConcept": { + "coding": [ + { + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.818994, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "text": "reviewed by expert panel" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15b7b", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-db2c78d7a2d84f6a9a8927fb296cb567" + } + ], + "id": "dv-62fab63a5932091e78bf6f6f", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "36584" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000107898.2" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8207,36 +8311,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-99d2b1819c554636b70c366c3f79f914" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -8245,18 +8341,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -8265,46 +8361,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-ddbfcfdb118b4385a9dad7e38d9b6da5" + } + ], + "id": "dv-62fab6665932091e78c1245b", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "125991" + "value": "90687" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001719551.2" + "value": "SCV000107200.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-99d2b1819c554636b70c366c3f79f914", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8312,21 +8416,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -8335,18 +8426,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -8355,17 +8446,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.11" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -8374,99 +8466,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "reviewed by expert panel" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-e1932783d03241559c7627fcde3fbec2" + } + ], + "id": "dv-62fab6665932091e78c11fa3", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "90368" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.11:32316588:T:G", - "display": "NC_000013.11:32316588:T:G" - } - ] - } - }, + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000106876.2" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "T" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -8475,38 +8571,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 32316588 - } + "valueCodeableConcept": { + "text": "reviewed by expert panel" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb2", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-e33b1b39b9074c3ab87f3695f3beb087" + } + ], + "id": "dv-62fab6665932091e78c1220d", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "90607" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000107124.2" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8514,36 +8626,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c7c0803976fd4ab881f1588c713419ff" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -8552,18 +8656,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -8572,46 +8676,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e7a8dac6a6aa45c5b219fea9973e34ab" + } + ], + "id": "dv-62fab6655932091e78c11631", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "89785" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002026104.2" + "value": "SCV000106257.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-c7c0803976fd4ab881f1588c713419ff", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8619,21 +8731,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -8642,18 +8741,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -8662,17 +8761,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.11" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -8681,155 +8781,159 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "reviewed by expert panel" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-e8e157f976b34a78ab1210328a2acd53" + } + ], + "id": "dv-62fab6655932091e78c11615", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "89773" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000106243.2" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" + } + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.11:32338917:A:G", - "display": "NC_000013.11:32338917:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "C4552100", + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "reviewed by expert panel" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32338917 - } - } + "reference": "Observation/dv-fc120b4aab9444d0b262a5d3036026b9" + } + ], + "id": "dv-62fab6645932091e78c10b92", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "89294" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000107969.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6655932091e78c11631", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8837,36 +8941,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e7a8dac6a6aa45c5b219fea9973e34ab" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -8875,18 +8971,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C4552100", - "display": "Lynch syndrome" + "display": "Lynch syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -8895,9 +8991,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -8906,35 +9002,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fcf9e127dc524dbab17c34123fd5aaf0" + } + ], + "id": "dv-62fab6655932091e78c11c6a", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89785" + "value": "90227" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106257.2" + "value": "SCV000106721.2" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e7a8dac6a6aa45c5b219fea9973e34ab", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8942,21 +9046,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -8965,18 +9057,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -8985,17 +9077,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "NC_000001.11", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -9004,66 +9096,29 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37037014:A:G", - "display": "NC_000003.12:37037014:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -9073,30 +9128,30 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueString": "ACTG" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000001.11:55039879:CTGCTGCTGCTGCTGCTGCTGCT:CTGCTGCTGCTGCTGCTGCTGCTGCT", + "display": "NC_000001.11:55039879:CTGCTGCTGCTGCTGCTGCTGCT:CTGCTGCTGCTGCTGCTGCTGCTGCT", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -9105,143 +9160,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 37037014 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf6f9a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "value": 55039878 } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-70b3a31ae2224e559d8be65a11a9eddb" - } - ], - "component": [ + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.121721 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36587" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107992.2" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6655932091e78c119bb", + "id": "dv-9bd8faa16b7f4b1d9a8d4c14b358b7db", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -9249,36 +9264,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-983532b4ef8b4928978bfaeba42af3db" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -9287,18 +9295,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "NC_000001.11", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -9307,46 +9314,167 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "coding": [ + { + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ + }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89983" + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106463.2" + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "T" + }, + { + "code": { + "coding": [ + { + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000001.11:55039973:G:T", + "display": "NC_000001.11:55039973:G:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" + } + ] + }, + "valueRange": { + "low": { + "value": 55039973 + } + } + }, + { + "code": { + "coding": [ + { + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" + } + ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { + "coding": [ + { + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" + } + ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.0119305 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] + } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-983532b4ef8b4928978bfaeba42af3db", + ], + "id": "dv-5c81355782d446179e37701af154f50b", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -9354,21 +9482,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -9377,18 +9493,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -9397,17 +9513,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -9416,18 +9532,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6705-3", - "display": "homozygous" + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -9436,18 +9552,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "A" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "T" + }, + { + "code": { + "coding": [ + { "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37048782:C:T", - "display": "NC_000003.12:37048782:C:T" + "code": "NC_000002.12:47803698:A:T", + "display": "NC_000002.12:47803698:A:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -9456,99 +9596,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 47803698 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.411752 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 37048782 - } } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6655932091e78c11615", + ], + "id": "dv-5071403516aa4a17871949bf246b8b5d", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -9556,36 +9700,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e8e157f976b34a78ab1210328a2acd53" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -9594,18 +9731,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -9614,46 +9750,167 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "coding": [ + { + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89773" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106243.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e8e157f976b34a78ab1210328a2acd53", + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "C" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, + { + "code": { + "coding": [ + { + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000002.12:47806411:C:G", + "display": "NC_000002.12:47806411:C:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" + } + ] + }, + "valueRange": { + "low": { + "value": 47806411 + } + } + }, + { + "code": { + "coding": [ + { + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" + } + ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } + }, + { + "code": { + "coding": [ + { + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" + } + ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.733985 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] + } + } + ], + "id": "dv-b8cc4e2fbe604134979c80e1aa8c4cee", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -9661,21 +9918,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -9684,18 +9929,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -9704,17 +9949,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -9723,18 +9968,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6705-3", - "display": "homozygous" + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -9743,18 +9988,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "C" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "T" + }, + { + "code": { + "coding": [ + { "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37031135:A:C", - "display": "NC_000003.12:37031135:A:C" + "code": "NC_000002.12:21002408:C:T", + "display": "NC_000002.12:21002408:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -9763,99 +10032,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 21002408 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.704884 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 37031135 - } } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15c01", + ], + "id": "dv-d675ed9e0e514a478542b503a5250ab3", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -9863,36 +10136,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-edfe8714ceaf4687910f600e46f6806e" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -9901,18 +10167,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -9921,83 +10186,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ + }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "C" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002026093.2" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c34f8c", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b5fde7b61b29434bb495e2bca5859063" - } - ], - "component": [ + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "T" + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "NC_000002.12:47797736:C:T", + "display": "NC_000002.12:47797736:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -10006,66 +10250,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 47797736 + } + } + }, + { + "code": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "251936" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001727625.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-b5fde7b61b29434bb495e2bca5859063", + "id": "dv-8154922662b44a9aa5260207fea8d5b6", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -10073,21 +10338,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -10096,18 +10349,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -10116,17 +10369,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.10" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -10135,99 +10388,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.10:11116123:C:T", - "display": "NC_000019.10:11116123:C:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000002.12:47803318:G:C", + "display": "NC_000002.12:47803318:G:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -10236,15 +10452,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 11116123 + "value": 47803318 } } }, @@ -10252,38 +10468,71 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.0756166, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf7276", + ], + "id": "dv-2439d4f778564bdd88dc95b2864fac18", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -10291,36 +10540,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-5940367f4ed843f59a836f0cdce1dafe" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -10329,18 +10571,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -10349,127 +10590,197 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "coding": [ + { + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ + }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36693" + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "T" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108381.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-5940367f4ed843f59a836f0cdce1dafe", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "C" + }, { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "code": { + "coding": [ + { + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000002.12:21009930:T:C", + "display": "NC_000002.12:21009930:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + }, + { + "code": { + "coding": [ + { + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" + } + ] + }, + "valueRange": { + "low": { + "value": 21009930 + } } - ] - }, - "component": [ + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } + }, + { + "code": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.995763 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" } ] } - }, + } + ], + "id": "dv-f2bfcff0b23a4c15a74aaeaef5faec4f", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" + } + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -10478,18 +10789,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:5997348:G:C", - "display": "NC_000007.14:5997348:G:C" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -10498,38 +10808,41 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, @@ -10539,18 +10852,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000002.12:47805797:T:C", + "display": "NC_000002.12:47805797:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -10559,15 +10872,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 5997348 + "value": 47805797 } } }, @@ -10575,143 +10888,71 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.8018, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10fbb", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-32bc0d97fc48469c8f3bf615dc186530" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89432" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108113.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", "id": "dv-32bc0d97fc48469c8f3bf615dc186530", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -10719,21 +10960,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -10742,18 +10971,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -10762,17 +10991,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -10781,18 +11010,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -10801,119 +11030,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "A" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47805797:T:C", - "display": "NC_000002.12:47805797:T:C" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000002.12:47444602:A:C", + "display": "NC_000002.12:47444602:A:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueRange": { + "low": { + "value": 47444602 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 47805797 - } } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc2", + ], + "id": "dv-4e13aba739b94934be7f63b77b87abf0", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -10921,36 +11162,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c7c0803976fd4ab881f1588c713419ff" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -10959,18 +11193,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -10979,83 +11212,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000494326.1" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf6f6f", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "A" + }, { - "reference": "Observation/dv-db2c78d7a2d84f6a9a8927fb296cb567" - } - ], - "component": [ + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "NC_000002.12:47476101:A:G", + "display": "NC_000002.12:47476101:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -11064,66 +11276,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 47476101 + } + } + }, + { + "code": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36584" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107898.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-db2c78d7a2d84f6a9a8927fb296cb567", + "id": "dv-acb6861a2ae345cdae082be1563a4a66", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -11131,21 +11364,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -11154,18 +11375,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -11174,17 +11395,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -11193,18 +11414,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -11213,96 +11434,59 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47783418:C:A", - "display": "NC_000002.12:47783418:C:A" - } - ] - } + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueString": "C" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "NC_000002.12:47785959:A:G", + "display": "NC_000002.12:47785959:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] - }, - "valueString": "A" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 47783418 + "value": 47785959 } } }, @@ -11310,143 +11494,71 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.14442, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66e5932091e78c176b0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-719286980a454cc792902098a0122614" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "128416" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000902556.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-719286980a454cc792902098a0122614", + "id": "dv-d83d284e564e4106a409fcd7bb222eb9", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -11454,21 +11566,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -11477,18 +11577,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -11497,17 +11597,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -11516,18 +11616,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -11536,135 +11636,147 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:21005954:C:T", - "display": "NC_000002.12:21005954:C:T" - } - ] - } + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueString": "C" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "NC_000002.12:47790890:A:G", + "display": "NC_000002.12:47790890:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 47790890 + } + } + }, + { + "code": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 21005954 - } + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.0372618 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.0700284, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6995932091e78c31f8b", + ], + "id": "dv-525568db5bbb42e79c7b9c4b5d27fd28", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -11672,36 +11784,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-9bd8faa16b7f4b1d9a8d4c14b358b7db" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -11710,18 +11815,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -11730,127 +11834,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "235043" }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000912224.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-9bd8faa16b7f4b1d9a8d4c14b358b7db", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000001.11" - } - ] - } + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "NC_000002.12:47790941:A:G", + "display": "NC_000002.12:47790941:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -11859,135 +11898,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000001.11:55039879:CTGCTGCTGCTGCTGCTGCTGCT:CTGCTGCTGCTGCTGCTGCTGCTGCT", - "display": "NC_000001.11:55039879:CTGCTGCTGCTGCTGCTGCTGCT:CTGCTGCTGCTGCTGCTGCTGCTGCT" - } - ] + "valueRange": { + "low": { + "value": 47790941 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "81258-6", - "display": "Sample VAF" + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "ACTG" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.134727 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 55039878 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.121721, - "system": "http://unitsofmeasure.org", - "code": "1" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf6fe4", + ], + "id": "dv-70b3a31ae2224e559d8be65a11a9eddb", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -11995,36 +12002,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-aab391f842a14a79865639fc25b95ff9" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - 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[ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "value": 0.6847 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 47795975 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.212977, - "system": "http://unitsofmeasure.org", - "code": "1" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6675932091e78c13034", + ], + "id": "dv-a71417cfb7164f2090e77f29a9ead21a", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -12318,36 +12220,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-d35a9e4b945a443abf237057131c03e5" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -12356,108 +12251,37 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "91356" }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108367.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-d35a9e4b945a443abf237057131c03e5", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -12466,57 +12290,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" - } - ] - } + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:5999497:T:C", - "display": "NC_000007.14:5999497:T:C" + "code": "NC_000002.12:47783418:C:A", + "display": "NC_000002.12:47783418:C:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -12525,99 +12334,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 47783418 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.14442 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 5999497 - } } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6655932091e78c11493", + ], + "id": "dv-db2c78d7a2d84f6a9a8927fb296cb567", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -12625,36 +12438,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-324e0f6400104fc4846edb4fa8d66008" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -12663,18 +12469,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -12683,88 +12488,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" - } - } - ], - "identifier": [ - { - "system": 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"48002-0", - "display": "Genomic Source Class" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -12773,57 +12508,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" - } - ] - } + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37025558:A:G", - "display": "NC_000003.12:37025558:A:G" + "code": "NC_000002.12:47783514:C:G", + "display": "NC_000002.12:47783514:C:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -12832,99 +12552,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 47783514 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.13896 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 37025558 - } } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17ccc", + ], + "id": "dv-49a4913593454c339fb981bd5144d9a6", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -12932,36 +12656,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-d47c74da1d8340e3976b600eedc794ac" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": 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"display": "Genomic Source Class" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -13080,37 +12726,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "C" + }, + { + "code": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.11" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "NC_000002.12:21005954:C:T", + "display": "NC_000002.12:21005954:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -13119,240 +12770,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.11:32340867:G:C", - "display": "NC_000013.11:32340867:G:C" - } - ] + "valueRange": { + "low": { + "value": 21005954 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "81258-6", - "display": "Sample VAF" + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.0700284 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32340867 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10f67", + ], + "id": "dv-719286980a454cc792902098a0122614", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, "subject": { "reference": "Patient/NB6TK329" }, - "derivedFrom": [ - { - "reference": "Observation/dv-db238eae873046a1bd607a546dc9381e" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": 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"coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -13360,21 +12874,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -13383,18 +12885,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -13403,17 +12905,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -13422,18 +12924,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -13442,119 +12944,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "C" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47805172:G:A", - "display": "NC_000002.12:47805172:G:A" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000002.12:47465141:C:T", + "display": "NC_000002.12:47465141:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueRange": { + "low": { + "value": 47465141 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 47805172 - } } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10f6f", + ], + "id": "dv-ddbfcfdb118b4385a9dad7e38d9b6da5", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -13562,36 +13076,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-3b3666df092d4e808a0d597a56a5022b" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -13600,18 +13107,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -13620,127 +13126,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "coding": [ + { + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89411" }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108091.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-3b3666df092d4e808a0d597a56a5022b", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" - } - ] - } + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "NC_000002.12:47785706:C:T", + "display": "NC_000002.12:47785706:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -13749,224 +13190,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47805186:T:C", - "display": "NC_000002.12:47805186:T:C" - } - ] + "valueRange": { + "low": { + "value": 47785706 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "81258-6", - "display": "Sample VAF" + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 47805186 - } } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10b92", + ], + "id": "dv-fc120b4aab9444d0b262a5d3036026b9", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, "subject": { "reference": "Patient/NB6TK329" }, - "derivedFrom": [ - { - "reference": "Observation/dv-fc120b4aab9444d0b262a5d3036026b9" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89294" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107969.2" - } - ] + ] + } } }, { "name": "variant", "resource": { - "resourceType": "Observation", - "id": "dv-fc120b4aab9444d0b262a5d3036026b9", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -13974,21 +13278,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -13997,18 +13289,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -14017,17 +13309,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -14036,66 +13328,29 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47785706:C:T", - "display": "NC_000002.12:47785706:C:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -14105,9 +13360,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, @@ -14117,18 +13372,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000002.12:47798554:C:T", + "display": "NC_000002.12:47798554:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -14137,143 +13392,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 47785706 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10fb4", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "value": 47798554 } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-a71417cfb7164f2090e77f29a9ead21a" - } - ], - "component": [ + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89429" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108111.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-a71417cfb7164f2090e77f29a9ead21a", + "id": "dv-37cd8d0c069d43cca4761374a718b6e8", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -14281,21 +13480,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -14304,18 +13491,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -14324,17 +13511,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -14343,18 +13530,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -14363,135 +13550,147 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47805735:CTATCTATCT:CTATCT", - "display": "NC_000002.12:47805735:CTATCTATCT:CTATCT" - } - ] - } + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueString": "ACTAT" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "NC_000002.12:21009322:G:A", + "display": "NC_000002.12:21009322:G:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] - }, - "valueString": "A" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 21009322 + } + } + }, + { + "code": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 47805734 - } + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.388555 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.6847, - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab68a5932091e78c28ec6", + ], + "id": "dv-b96b0bdcbc3a4a68913378136736b773", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -14499,36 +13698,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f2d0de4c461c487fa0d7b2b0a9034361" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -14537,18 +13729,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -14557,83 +13748,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "200916" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001729839.2" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c05bb5adae894ebc865a6808c7685992" - } - ], - "component": [ + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "A" + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "NC_000002.12:21041027:G:A", + "display": "NC_000002.12:21041027:G:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -14642,66 +13812,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 21041027 + } + } + }, + { + "code": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.25802 } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001000149.4" + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] + } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-c05bb5adae894ebc865a6808c7685992", + ], + "id": "dv-1692d4f52d4944a391a1e1e57347d8eb", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -14709,21 +13916,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -14732,18 +13927,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -14752,17 +13947,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.11" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -14771,99 +13966,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.11:32355249:T:C", - "display": "NC_000013.11:32355249:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000002.12:47429661:G:A", + "display": "NC_000002.12:47429661:G:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -14872,15 +14030,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 32355249 + "value": 47429661 } } }, @@ -14888,38 +14046,71 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.994876, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6725932091e78c1a029", + ], + "id": "dv-210349083123421e9899d9f21af3ef71", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -14927,36 +14118,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-57863b6706444b2e9fabc5d5808df40a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -14965,18 +14149,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -14985,88 +14168,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "137691" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002505088.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-57863b6706444b2e9fabc5d5808df40a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "A" + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "NC_000002.12:47445429:G:A", + "display": "NC_000002.12:47445429:G:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -15075,37 +14232,117 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 47445429 + } + } + }, + { + "code": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000017.11" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] + } + } + ], + "id": "dv-7dcdefbf50b7446eb461e5d998247478", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" + } + ] + }, + "component": [ + { + "code": { + "coding": [ + { + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -15114,18 +14351,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000017.11:7676482:G:C", - "display": "NC_000017.11:7676482:G:C" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -15134,26 +14370,29 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -15163,30 +14402,30 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000002.12:47805172:G:A", + "display": "NC_000002.12:47805172:G:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -15195,15 +14434,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 7676482 + "value": 47805172 } } }, @@ -15211,143 +14450,71 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.673405, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6655932091e78c11bb9", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-aa7bc4cb064c41b8939860b917dde5af" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90146" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106634.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-aa7bc4cb064c41b8939860b917dde5af", + "id": "dv-db238eae873046a1bd607a546dc9381e", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -15355,21 +14522,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -15378,18 +14533,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -15398,17 +14553,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -15417,18 +14572,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -15437,119 +14592,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37001468:A:C", - "display": "NC_000003.12:37001468:A:C" - } - ] - } + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "NC_000002.12:47476887:G:C", + "display": "NC_000002.12:47476887:G:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 47476887 + } + } + }, + { + "code": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 37001468 - } + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf6fd4", + ], + "id": "dv-4bde3f4b60a843a88d84e9974aa86fa7", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -15557,36 +14724,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b8cc4e2fbe604134979c80e1aa8c4cee" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -15595,18 +14755,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -15615,83 +14774,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36594" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000052939.2" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf6fdb", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, { - "reference": "Observation/dv-aab391f842a14a79865639fc25b95ff9" - } - ], - "component": [ + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "T" + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "NC_000002.12:47789756:G:T", + "display": "NC_000002.12:47789756:G:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -15700,66 +14838,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 47789756 + } + } + }, + { + "code": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36597" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000052942.2" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6665932091e78c12386", + "id": "dv-6b10bc016d794b2d891a2da2b7b49512", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -15767,36 +14926,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-7dcdefbf50b7446eb461e5d998247478" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -15805,18 +14957,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -15825,46 +14976,151 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "coding": [ + { + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90599" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107117.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-7dcdefbf50b7446eb461e5d998247478", + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "T" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "A" + }, + { + "code": { + "coding": [ + { + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000002.12:47791174:T:A", + "display": "NC_000002.12:47791174:T:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" + } + ] + }, + "valueRange": { + "low": { + "value": 47791174 + } + } + }, + { + "code": { + "coding": [ + { + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" + } + ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] + } + } + ], + "id": "dv-49c6c5a200fb42fba2c02268d74d00a3", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -15872,21 +15128,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -15895,18 +15139,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -15915,17 +15159,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -15934,18 +15178,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -15954,119 +15198,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "T" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47445429:G:A", - "display": "NC_000002.12:47445429:G:A" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000002.12:47439698:T:C", + "display": "NC_000002.12:47439698:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueRange": { + "low": { + "value": 47439698 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 47445429 - } } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66e5932091e78c17717", + ], + "id": "dv-e33b1b39b9074c3ab87f3695f3beb087", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -16074,36 +15330,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-1692d4f52d4944a391a1e1e57347d8eb" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -16112,18 +15361,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -16132,103 +15380,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ + }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "128422" + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "T" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000902527.1" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf3", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-edfe8714ceaf4687910f600e46f6806e" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "C" + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "NC_000002.12:47791516:T:C", + "display": "NC_000002.12:47791516:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -16237,151 +15444,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001000460.4" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab7095932091e78c75e4d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "valueRange": { + "low": { + "value": 47791516 } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f2bfcff0b23a4c15a74aaeaef5faec4f" - } - ], - "component": [ + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "1168905" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002053227.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f2bfcff0b23a4c15a74aaeaef5faec4f", + "id": "dv-234ee4ca3da04ab39f5ebfed027792dd", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -16389,21 +15532,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -16412,18 +15543,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -16432,17 +15563,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -16451,66 +15582,29 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:21009930:T:C", - "display": "NC_000002.12:21009930:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -16520,9 +15614,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, @@ -16532,18 +15626,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000002.12:47792345:T:C", + "display": "NC_000002.12:47792345:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -16552,15 +15646,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 21009930 + "value": 47792345 } } }, @@ -16568,38 +15662,71 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.995763, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6905932091e78c2c79a", + ], + "id": "dv-1aa0fdfa74344f23b55e811414e4dcdf", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -16607,36 +15734,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e28737e34fd843fbbe1717b56b96d1f8" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -16645,18 +15765,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -16665,83 +15784,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "218461" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000257707.2" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6395932091e78bf6b0a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "T" + }, { - "reference": "Observation/dv-437c728d910a46189036896c9a3fe97f" - } - ], - "component": [ + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "C" + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "NC_000002.12:47795975:T:C", + "display": "NC_000002.12:47795975:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -16750,66 +15848,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 47795975 + } + } + }, + { + "code": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.212977 } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36542" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000052882.2" + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] + } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-437c728d910a46189036896c9a3fe97f", + ], + "id": "dv-aab391f842a14a79865639fc25b95ff9", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -16817,21 +15952,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -16840,18 +15963,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -16860,17 +15983,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -16879,99 +16002,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37042248:A:G", - "display": "NC_000003.12:37042248:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000002.12:47805186:T:C", + "display": "NC_000002.12:47805186:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -16980,15 +16066,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 37042248 + "value": 47805186 } } }, @@ -16996,38 +16082,71 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.370828, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf725d", + ], + "id": "dv-3b3666df092d4e808a0d597a56a5022b", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -17035,36 +16154,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-5940367f4ed843f59a836f0cdce1dafe" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -17073,18 +16185,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "NC_000002.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -17093,83 +16204,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36693" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000053039.2" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6655932091e78c1146d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "TAA" + }, { - "reference": "Observation/dv-89eb7b13687a4828baa470fb82be0c0d" - } - ], - "component": [ + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "T" + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "NC_000002.12:47414420:AAAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAA", + "display": "NC_000002.12:47414420:AAAAAAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAA", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -17178,66 +16268,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 47414419 + } + } + }, + { + "code": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89615" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106073.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-89eb7b13687a4828baa470fb82be0c0d", + "id": "dv-dd6a5ae0dbc24360aea5a7c161101a68", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -17245,21 +16356,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -17268,18 +16367,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -17288,17 +16387,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "NC_000003.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -17307,18 +16406,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6705-3", - "display": "homozygous" + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -17327,119 +16426,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "A" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37020548:T:C", - "display": "NC_000003.12:37020548:T:C" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000003.12:37001468:A:C", + "display": "NC_000003.12:37001468:A:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueRange": { + "low": { + "value": 37001468 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 37020548 - } } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6665932091e78c12377", + ], + "id": "dv-aa7bc4cb064c41b8939860b917dde5af", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -17447,36 +16558,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-4e13aba739b94934be7f63b77b87abf0" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -17485,18 +16589,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "NC_000003.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -17505,127 +16608,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "coding": [ + { + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90609" }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107126.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-4e13aba739b94934be7f63b77b87abf0", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" - } - ] - } + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "NC_000003.12:37031135:A:C", + "display": "NC_000003.12:37031135:A:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -17634,119 +16672,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47444602:A:C", - "display": "NC_000002.12:47444602:A:C" - } - ] + "valueRange": { + "low": { + "value": 37031135 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "81258-6", - "display": "Sample VAF" + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 47444602 - } } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6655932091e78c11695", + ], + "id": "dv-e8e157f976b34a78ab1210328a2acd53", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -17754,36 +16760,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-86d0233b22f3488197627b36c7594a73" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -17792,108 +16791,37 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "NC_000003.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89830" }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106300.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-86d0233b22f3488197627b36c7594a73", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -17902,37 +16830,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "A" + }, + { + "code": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "NC_000003.12:37007141:A:G", + "display": "NC_000003.12:37007141:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -17941,224 +16874,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37041382:T:C", - "display": "NC_000003.12:37041382:T:C" - } - ] + "valueRange": { + "low": { + "value": 37007141 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "81258-6", - "display": "Sample VAF" + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, - "valueString": "T" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 37041382 - } } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66e5932091e78c17733", + ], + "id": "dv-fcf9e127dc524dbab17c34123fd5aaf0", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, "subject": { "reference": "Patient/NB6TK329" }, - "derivedFrom": [ - { - "reference": "Observation/dv-b96b0bdcbc3a4a68913378136736b773" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "128425" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000902523.1" - } - ] + ] + } } }, { "name": "variant", "resource": { - "resourceType": "Observation", - "id": "dv-b96b0bdcbc3a4a68913378136736b773", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -18166,21 +16962,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -18189,18 +16973,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -18209,17 +16993,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000003.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -18228,99 +17012,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:21009322:G:A", - "display": "NC_000002.12:21009322:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000003.12:37025558:A:G", + "display": "NC_000003.12:37025558:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -18329,15 +17076,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 21009322 + "value": 37025558 } } }, @@ -18345,38 +17092,71 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.388555, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10df7", + ], + "id": "dv-324e0f6400104fc4846edb4fa8d66008", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -18384,36 +17164,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-2439d4f778564bdd88dc95b2864fac18" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -18422,18 +17195,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "NC_000003.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -18442,127 +17214,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "coding": [ + { + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89345" }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108022.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-2439d4f778564bdd88dc95b2864fac18", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" - } - ] - } + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "NC_000003.12:37037014:A:G", + "display": "NC_000003.12:37037014:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -18571,224 +17278,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47803318:G:C", - "display": "NC_000002.12:47803318:G:C" - } - ] + "valueRange": { + "low": { + "value": 37037014 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "81258-6", - "display": "Sample VAF" + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 47803318 - } } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6655932091e78c11c6a", + ], + "id": "dv-e7a8dac6a6aa45c5b219fea9973e34ab", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, "subject": { "reference": "Patient/NB6TK329" }, - "derivedFrom": [ - { - "reference": "Observation/dv-fcf9e127dc524dbab17c34123fd5aaf0" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - 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"http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -18796,21 +17366,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -18819,18 +17377,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -18839,17 +17397,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "NC_000003.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -18858,66 +17416,29 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37007141:A:G", - "display": "NC_000003.12:37007141:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "display": "homozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -18927,9 +17448,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, @@ -18939,18 +17460,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000003.12:37042248:A:G", + "display": "NC_000003.12:37042248:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -18959,38 +17480,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 37007141 + "value": 37042248 } } + }, + { + "code": { + "coding": [ + { + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" + } + ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } + }, + { + "code": { + "coding": [ + { + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" + } + ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.370828 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] + } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e3", + ], + "id": "dv-437c728d910a46189036896c9a3fe97f", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -18998,36 +17584,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c05bb5adae894ebc865a6808c7685992" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -19036,18 +17615,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "NC_000003.12", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -19056,83 +17634,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002025816.2" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c3549c", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "C" + }, { - "reference": "Observation/dv-37304b7e844c41258d4a25a6dffada5b" - } - ], - "component": [ + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "A" + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "NC_000003.12:37015498:C:A", + "display": "NC_000003.12:37015498:C:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -19141,66 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"coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001461329.1" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6335932091e78bf3e30", + "id": "dv-994f4ecf114a4bbb92bdb40776afc9b3", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -19208,36 +17786,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-3bbaa1e62567438db8586df47ee86d51" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": 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start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 32338917 + } + } + }, + { + "code": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" + } + ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } + }, + { + "code": { + "coding": [ + { + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.994359 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90607" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107124.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e33b1b39b9074c3ab87f3695f3beb087", + "id": "dv-c7c0803976fd4ab881f1588c713419ff", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -19741,21 +20492,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -19764,18 +20503,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -19784,17 +20523,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000013.11", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -19803,78 +20542,41 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47439698:T:C", - "display": "NC_000002.12:47439698:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, @@ -19884,18 +20586,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000013.11:32340867:G:C", + "display": "NC_000013.11:32340867:G:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -19904,248 +20606,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 47439698 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6395932091e78bf6afa", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "value": 32340867 } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-437c728d910a46189036896c9a3fe97f" - } - ], - "component": [ + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.994199 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36542" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106295.2" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6665932091e78c11f9b", + "id": "dv-d47c74da1d8340e3976b600eedc794ac", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, "subject": { "reference": "Patient/NB6TK329" }, - "derivedFrom": [ - { - "reference": "Observation/dv-994f4ecf114a4bbb92bdb40776afc9b3" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90366" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106871.2" - } - ] + ] + } } }, { "name": "variant", "resource": { - "resourceType": "Observation", - "id": "dv-994f4ecf114a4bbb92bdb40776afc9b3", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -20153,21 +20710,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -20176,18 +20721,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -20196,17 +20741,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "NC_000013.11", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -20215,18 +20760,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6705-3", - "display": "homozygous" + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -20235,79 +20780,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:37015498:C:A", - "display": "NC_000003.12:37015498:C:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000013.11:32338161:T:C", + "display": "NC_000013.11:32338161:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -20316,143 +20824,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 37015498 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf264e", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "value": 32338161 } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-5c81355782d446179e37701af154f50b" - } - ], - "component": [ + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.174603 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "2878" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000690958.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-5c81355782d446179e37701af154f50b", + "id": "dv-edfe8714ceaf4687910f600e46f6806e", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -20460,21 +20928,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -20483,18 +20939,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -20503,17 +20959,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000001.11" + "code": "NC_000013.11", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -20522,99 +20978,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000001.11:55039973:G:T", - "display": "NC_000001.11:55039973:G:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000013.11:32355249:T:C", + "display": "NC_000013.11:32355249:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -20623,15 +21042,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 55039973 + "value": 32355249 } } }, @@ -20639,143 +21058,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.0119305, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6665932091e78c1262d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-acb6861a2ae345cdae082be1563a4a66" - } - ], - "component": [ + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.994876 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90846" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107374.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-acb6861a2ae345cdae082be1563a4a66", + "id": "dv-c05bb5adae894ebc865a6808c7685992", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -20783,21 +21146,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -20806,18 +21157,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -20826,17 +21177,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000013.11", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -20845,78 +21196,41 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47476101:A:G", - "display": "NC_000002.12:47476101:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, @@ -20926,18 +21240,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000013.11:32316588:T:G", + "display": "NC_000013.11:32316588:T:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -20946,143 +21260,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 47476101 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6435932091e78bfc9ac", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "value": 32316588 } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-5071403516aa4a17871949bf246b8b5d" - } - ], - "component": [ + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42471" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108065.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-5071403516aa4a17871949bf246b8b5d", + "id": "dv-99d2b1819c554636b70c366c3f79f914", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -21090,21 +21348,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -21113,18 +21359,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -21133,17 +21379,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000017.11", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -21152,260 +21398,167 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47803698:A:T", - "display": "NC_000002.12:47803698:A:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 47803698 - } - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "NC_000017.11:7676153:G:C", + "display": "NC_000017.11:7676153:G:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] - }, - "valueQuantity": { - "value": 0.411752, - "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cbd", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c7c0803976fd4ab881f1588c713419ff" - } - ], - "component": [ + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "valueRange": { + "low": { + "value": 7676153 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.668165 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000635377.5" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab63a5932091e78bf6f6e", + "id": "dv-3bbaa1e62567438db8586df47ee86d51", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -21413,36 +21566,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-db2c78d7a2d84f6a9a8927fb296cb567" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -21451,18 +21597,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "NC_000017.11", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -21471,83 +21616,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "36584" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000052928.2" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6655932091e78c11355", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, { - "reference": "Observation/dv-8154922662b44a9aa5260207fea8d5b6" - } - ], - "component": [ + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "C" + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "NC_000017.11:7676482:G:C", + "display": "NC_000017.11:7676482:G:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -21556,66 +21680,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 7676482 + } + } + }, + { + "code": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.673405 } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89544" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000108233.2" + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] + } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-8154922662b44a9aa5260207fea8d5b6", + ], + "id": "dv-57863b6706444b2e9fabc5d5808df40a", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -21623,21 +21784,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -21646,18 +21795,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -21666,17 +21815,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000019.10", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -21685,38 +21834,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "A" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47797736:C:T", - "display": "NC_000002.12:47797736:C:T" + "code": "NC_000019.10:11123264:A:G", + "display": "NC_000019.10:11123264:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -21725,99 +21898,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 11123264 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.781146 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 47797736 - } } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17ce1", + ], + "id": "dv-37304b7e844c41258d4a25a6dffada5b", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -21825,36 +22002,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-d47c74da1d8340e3976b600eedc794ac" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -21863,18 +22033,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "NC_000019.10", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -21883,103 +22052,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000494339.1" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-d47c74da1d8340e3976b600eedc794ac" - } - ], - "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "G" + }, + { + "code": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "NC_000019.10:11131630:G:C", + "display": "NC_000019.10:11131630:G:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -21988,151 +22116,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000635514.5" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6645932091e78c10b95", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "valueRange": { + "low": { + "value": 11131630 } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-49a4913593454c339fb981bd5144d9a6" - } - ], - "component": [ + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.818994 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "89295" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000107970.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-49a4913593454c339fb981bd5144d9a6", + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] + } + } + ], + "id": "dv-6f1550b878b740c29dae310d745dbc76", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -22140,21 +22220,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -22163,18 +22231,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -22183,17 +22251,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.12" + "code": "NC_000019.10", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -22202,18 +22270,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -22222,58 +22290,21 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000002.12:47783514:C:G", - "display": "NC_000002.12:47783514:C:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, @@ -22283,18 +22314,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.10:11113588:A:G", + "display": "NC_000019.10:11113588:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -22303,15 +22334,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 47783514 + "value": 11113588 } } }, @@ -22319,143 +22350,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.13896, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6655932091e78c11a58", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-396515d9058748f2a3ce8d4e5149620b" - } - ], - "component": [ + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.632026 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552100", - "display": "Lynch syndrome" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueCodeableConcept": { - "text": "reviewed by expert panel" } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "90024" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000106504.2" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-396515d9058748f2a3ce8d4e5149620b", + "id": "dv-f2d0de4c461c487fa0d7b2b0a9034361", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -22463,21 +22438,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -22486,18 +22449,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -22506,17 +22469,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.12" + "code": "NC_000019.10", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -22525,18 +22488,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -22545,18 +22508,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "C" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "T" + }, + { + "code": { + "coding": [ + { "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.12:36997279:C:T", - "display": "NC_000003.12:36997279:C:T" + "code": "NC_000019.10:11116123:C:T", + "display": "NC_000019.10:11116123:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -22565,81 +22552,94 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 11116123 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.0756166 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 36997279 - } - } } - ] + ], + "id": "dv-b5fde7b61b29434bb495e2bca5859063", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_dx_implications/4.json b/tests/expected_outputs/find_subject_dx_implications/4.json index dc8e014fb..3c45dcae7 100644 --- a/tests/expected_outputs/find_subject_dx_implications/4.json +++ b/tests/expected_outputs/find_subject_dx_implications/4.json @@ -1,23 +1,14 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "implication", "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf2329", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -25,36 +16,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6668-3", - "display": "Pathogenic" + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -63,18 +46,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C3469186", - "display": "Hemochromatosis type 1" + "display": "Hemochromatosis t", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -83,9 +66,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -94,6 +77,12 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], + "id": "dv-62fab6305932091e78bf231e", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -101,28 +90,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001251532.1" + "value": "SCV000893709.1" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e6b9e50014b24ebe81a0504cbba79282", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG02657" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -130,21 +121,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG02657" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -153,37 +131,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000006.11" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -192,18 +151,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "C3469186", + "display": "Hemochromatosis type 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -212,135 +171,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000006.11:26091178:C:G", - "display": "NC_000006.11:26091178:C:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "text": "criteria provided, single submitter" } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "C" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "G" - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], + "id": "dv-62fab6305932091e78bf230d", + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 26091178 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "10" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.10924, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV002038504.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf2317", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG02657" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -348,36 +226,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6668-3", - "display": "Pathogenic" + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -386,18 +256,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C3469186", - "display": "Hemochromatosis type 1" + "display": "Hemochromatosis type 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -406,9 +276,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -417,6 +287,12 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], + "id": "dv-62fab6305932091e78bf230e", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -424,28 +300,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001368348.2" + "value": "SCV001137061.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf230e", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG02657" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -453,36 +331,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6668-3", - "display": "Pathogenic" + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -491,18 +361,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C3469186", - "display": "Hemochromatosis type 1" + "display": "Hemochromatosis type 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -511,9 +381,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -522,6 +392,12 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], + "id": "dv-62fab6305932091e78bf2312", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -529,28 +405,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001137061.1" + "value": "SCV002499222.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf231b", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG02657" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -558,36 +436,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6668-3", - "display": "Pathogenic" + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -596,18 +466,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C3469186", - "display": "Hemochromatosis type 1" + "display": "Hemochromatosis type 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -616,9 +486,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -627,35 +497,43 @@ } } ], - "identifier": [ + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], + "id": "dv-62fab6305932091e78bf2317", + "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", "value": "10" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000693430.2" + "value": "SCV001368348.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf232b", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG02657" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -663,36 +541,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6668-3", - "display": "Pathogenic" + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -701,18 +571,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C3469186", - "display": "Hemochromatosis type 1" + "display": "Hemochromatosis type 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -721,9 +591,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -732,6 +602,12 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], + "id": "dv-62fab6305932091e78bf231b", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -739,28 +615,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001523197.1" + "value": "SCV000693430.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf2330", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG02657" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -768,36 +646,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6668-3", - "display": "Pathogenic" + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -806,18 +676,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C3469186", - "display": "Hemochromatosis type 1" + "display": "Hemochromatosis type 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -826,9 +696,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -837,6 +707,12 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], + "id": "dv-62fab6305932091e78bf231f", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -844,28 +720,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000206973.2" + "value": "SCV002028310.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf2316", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG02657" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -873,36 +751,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6668-3", - "display": "Pathogenic" + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -911,18 +781,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C3469186", - "display": "Hemochromatosis type 1" + "display": "Hemochromatosis type 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -931,17 +801,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], + "id": "dv-62fab6305932091e78bf2322", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -949,28 +825,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000245789.1" + "value": "SCV001194094.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf232f", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG02657" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -978,36 +856,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6668-3", - "display": "Pathogenic" + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -1016,18 +886,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C3469186", - "display": "Hemochromatosis type 1" + "display": "Hemochromatosis type 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1036,17 +906,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], + "id": "dv-62fab6305932091e78bf2326", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -1054,28 +930,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000020169.4" + "value": "SCV001519563.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf232c", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG02657" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1083,36 +961,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6668-3", - "display": "Pathogenic" + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -1121,18 +991,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C3469186", - "display": "Hemochromatosis type 1" + "display": "Hemochromatosis type 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1141,9 +1011,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -1152,6 +1022,12 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], + "id": "dv-62fab6305932091e78bf2329", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -1159,28 +1035,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000223933.2" + "value": "SCV001251532.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf231e", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG02657" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1188,36 +1066,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6668-3", - "display": "Pathogenic" + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -1226,18 +1096,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C3469186", - "display": "Hemochromatosis t" + "display": "Hemochromatosis type 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1246,9 +1116,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -1257,6 +1127,12 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], + "id": "dv-62fab6305932091e78bf232b", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -1264,28 +1140,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000893709.1" + "value": "SCV001523197.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf231f", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG02657" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1293,36 +1171,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6668-3", - "display": "Pathogenic" + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -1331,18 +1201,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C3469186", - "display": "Hemochromatosis type 1" + "display": "Hemochromatosis type 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1351,9 +1221,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -1362,6 +1232,12 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], + "id": "dv-62fab6305932091e78bf232c", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -1369,28 +1245,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002028310.1" + "value": "SCV000223933.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf2326", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG02657" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1398,36 +1276,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6668-3", - "display": "Pathogenic" + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -1436,18 +1306,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C3469186", - "display": "Hemochromatosis type 1" + "display": "Hemochromatosis type 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1456,9 +1326,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -1467,6 +1337,12 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], + "id": "dv-62fab6305932091e78bf2330", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -1474,28 +1350,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001519563.1" + "value": "SCV000206973.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf230d", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG02657" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1503,36 +1381,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6668-3", - "display": "Pathogenic" + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -1541,18 +1411,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C3469186", - "display": "Hemochromatosis type 1" + "display": "Hemochromatosis type 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1561,17 +1431,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], + "id": "dv-62fab6305932091e78bf2316", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -1579,28 +1455,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002038504.1" + "value": "SCV000245789.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf2312", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG02657" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1608,36 +1486,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6668-3", - "display": "Pathogenic" + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -1646,18 +1516,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C3469186", - "display": "Hemochromatosis type 1" + "display": "Hemochromatosis type 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1666,17 +1536,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" + } + ], + "id": "dv-62fab6305932091e78bf232f", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -1684,28 +1560,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002499222.1" + "value": "SCV000020169.4" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6305932091e78bf2322", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG02657" + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1713,36 +1591,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/HG02657" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e6b9e50014b24ebe81a0504cbba79282" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -1751,18 +1622,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3469186", - "display": "Hemochromatosis type 1" + "code": "NC_000006.11", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -1771,28 +1641,158 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ + }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "10" + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "C" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001194094.2" + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, + { + "code": { + "coding": [ + { + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000006.11:26091178:C:G", + "display": "NC_000006.11:26091178:C:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" + } + ] + }, + "valueRange": { + "low": { + "value": 26091178 + } + } + }, + { + "code": { + "coding": [ + { + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" + } + ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { + "coding": [ + { + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" + } + ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.10924 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] + } } - ] + ], + "id": "dv-e6b9e50014b24ebe81a0504cbba79282", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/HG02657" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_dx_implications/5.json b/tests/expected_outputs/find_subject_dx_implications/5.json index df76b8c23..96b024a8f 100644 --- a/tests/expected_outputs/find_subject_dx_implications/5.json +++ b/tests/expected_outputs/find_subject_dx_implications/5.json @@ -1,23 +1,14 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "implication", "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bef", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -25,36 +16,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA26332-9", + "display": "Likely pathogenic", + "system": "http://loinc.org" } ] } @@ -63,18 +46,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0949658", + "display": "Primary familial hypertrophic cardiomyopathy", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -83,9 +66,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -94,35 +77,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "id": "dv-62fab6355932091e78bf4ad6", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000146298.1" + "value": "SCV000188798.1" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-c2f729c9baee4e9290dfc7dae09d497f", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -130,21 +121,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -153,37 +131,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "code": "LA26332-9", + "display": "Likely pathogenic", + "system": "http://loinc.org" } ] } @@ -192,18 +151,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "CN517202", + "display": "not provided", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -212,135 +171,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32912298:T:C", - "display": "NC_000013.10:32912298:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "text": "no assertion criteria provided" } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "C" - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "id": "dv-62fab6355932091e78bf4afb", + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 32912298 - } - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "14095" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.174603, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001739623.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf1", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -348,36 +226,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA26333-7", + "display": "Uncertain significance", + "system": "http://loinc.org" } ] } @@ -386,18 +256,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C1527349", + "display": "Ductal breast carcinoma", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -406,46 +276,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "id": "dv-62fab6705932091e78c186e5", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000202285.7" + "value": "SCV000258682.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf3", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -453,36 +331,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA26333-7", + "display": "Uncertain significance", + "system": "http://loinc.org" } ] } @@ -491,18 +361,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -511,46 +381,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" + } + ], + "id": "dv-62fab66c5932091e78c15a84", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "125927" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001000460.4" + "value": "SCV000145775.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf5", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -558,36 +436,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA26333-7", + "display": "Uncertain significance", + "system": "http://loinc.org" } ] } @@ -596,18 +466,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "CN517202", + "display": "not provided", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -616,9 +486,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -627,35 +497,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda17", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001551831.1" + "value": "SCV001551199.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf9", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -663,36 +541,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA26334-5", + "display": "Likely benign", + "system": "http://loinc.org" } ] } @@ -701,18 +571,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -721,9 +591,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -732,35 +602,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-25751058304a4b40a5254642589509ae" + } + ], + "id": "dv-62fab6a85932091e78c3bb4e", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "328064" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000693636.1" + "value": "SCV000987015.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15c04", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -768,36 +646,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA26334-5", + "display": "Likely benign", + "system": "http://loinc.org" } ] } @@ -806,18 +676,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -826,9 +696,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -837,35 +707,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-57370e44f9884d8cb43661abf73c23c3" + } + ], + "id": "dv-62fab6a85932091e78c3bb56", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "328070" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000744444.1" + "value": "SCV000987013.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15c05", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -873,36 +751,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA26334-5", + "display": "Likely benign", + "system": "http://loinc.org" } ] } @@ -911,18 +781,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0027672", - "display": "Hereditary cancer-predisposing syndrome" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -931,9 +801,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -942,35 +812,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-904b6ac36b25461ea7a2304093bc6fec" + } + ], + "id": "dv-62fab6a85932091e78c3bb4a", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "328058" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000185213.5" + "value": "SCV000987012.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15c08", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -978,36 +856,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA26334-5", + "display": "Likely benign", + "system": "http://loinc.org" } ] } @@ -1016,18 +886,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1036,9 +906,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -1047,35 +917,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-930a27aa386d4cb8bff1e437040afb45" + } + ], + "id": "dv-62fab6a85932091e78c3bb58", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "328072" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000743289.1" + "value": "SCV000987014.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf2", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1083,36 +961,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA26334-5", + "display": "Likely benign", + "system": "http://loinc.org" } ] } @@ -1121,18 +991,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1141,46 +1011,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-d5e6a6a584a44454901740ac1d9c4b1f" + } + ], + "id": "dv-62fab6a85932091e78c3bb6b", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "328089" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000778666.1" + "value": "SCV000410580.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf6", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1188,36 +1066,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -1226,18 +1096,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0007194", + "display": "Hypertrophic cardiomyopathy", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1246,9 +1116,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -1257,35 +1127,43 @@ } } ], - "identifier": [ + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "id": "dv-62fab6355932091e78bf4adf", + "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000301763.1" + "value": "SCV000546190.6" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf7", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1293,36 +1171,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -1331,18 +1201,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0007194", + "display": "Hypertrophic cardiomyopathy", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1351,46 +1221,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "id": "dv-62fab6355932091e78bf4ae3", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000733249.1" + "value": "SCV000059423.7" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bfa", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1398,36 +1276,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -1436,18 +1306,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0007194", + "display": "Hypertrophic cardiomyopathy", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1456,46 +1326,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "id": "dv-62fab6355932091e78bf4aea", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000195977.1" + "value": "SCV000564425.4" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bfd", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1503,36 +1381,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -1541,18 +1411,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "C0020445", + "display": "Familial hypercholesterolemia", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1561,9 +1431,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -1572,35 +1442,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "id": "dv-62fab6315932091e78bf2a71", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "3683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000602744.6" + "value": "SCV000544678.5" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bff", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1608,36 +1486,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -1646,18 +1516,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0027672", - "display": "Hereditary cancer-predisposing syndrome" + "code": "C0020445", + "display": "Familial hypercholesterolemia", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1666,46 +1536,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "id": "dv-62fab6315932091e78bf2a80", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "3683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002533822.1" + "value": "SCV002086359.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15c00", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1713,36 +1591,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -1751,18 +1621,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1771,9 +1641,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -1782,35 +1652,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "id": "dv-62fab6315932091e78bf2a6e", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "3683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000494320.1" + "value": "SCV001653581.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15c02", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1818,36 +1696,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -1856,18 +1726,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1876,46 +1746,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "id": "dv-62fab6315932091e78bf2a75", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "3683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001953719.1" + "value": "SCV000294463.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bed", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1923,36 +1801,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -1961,18 +1831,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -1981,9 +1851,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -1992,35 +1862,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "id": "dv-62fab6315932091e78bf2a78", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "3683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000154051.1" + "value": "SCV000583630.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf0", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2028,36 +1906,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -2066,18 +1936,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0346153", - "display": "Familial cancer of breast" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -2086,9 +1956,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -2097,35 +1967,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "id": "dv-62fab6315932091e78bf2a7a", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "3683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000541022.1" + "value": "SCV000607415.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf8", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2133,36 +2011,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -2171,18 +2041,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -2191,9 +2061,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -2202,35 +2072,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "id": "dv-62fab6315932091e78bf2a7b", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "3683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000538459.1" + "value": "SCV000588484.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bfc", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2238,36 +2116,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -2276,18 +2146,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -2296,46 +2166,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "id": "dv-62fab6315932091e78bf2a7e", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "3683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001906228.1" + "value": "SCV000987040.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bfe", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2343,36 +2221,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -2381,18 +2251,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -2401,9 +2271,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -2412,35 +2282,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "id": "dv-62fab6315932091e78bf2a7f", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "3683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000586945.1" + "value": "SCV000503101.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15beb", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2448,36 +2326,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -2486,18 +2356,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -2506,9 +2376,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -2517,35 +2387,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "id": "dv-62fab6315932091e78bf2a76", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "3683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000189304.1" + "value": "SCV002017112.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bee", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2553,36 +2431,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -2591,18 +2461,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -2611,46 +2481,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "no assertion criteria provided" } } ], - "identifier": [ + "derivedFrom": [ { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" - }, + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "id": "dv-62fab6315932091e78bf2a7c", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "3683" + }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000245028.1" + "value": "SCV000606015.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bf4", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2658,36 +2536,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -2696,18 +2566,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0027672", - "display": "Hereditary cancer-predisposing syndrome" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -2716,46 +2586,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "id": "dv-62fab6315932091e78bf2a82", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "3683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000537340.1" + "value": "SCV000024033.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15bfb", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2763,36 +2641,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -2801,18 +2671,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C1838457", - "display": "Fanconi anemia complementation group D1" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -2821,46 +2691,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "id": "dv-62fab6315932091e78bf2a79", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "3683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000383688.3" + "value": "SCV002506409.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15c01", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2868,36 +2746,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -2906,18 +2776,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C0878544", + "display": "Cardiomyopathy", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -2926,9 +2796,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -2937,35 +2807,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "id": "dv-62fab6355932091e78bf4b17", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002026093.2" + "value": "SCV001352585.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15c03", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2973,36 +2851,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -3011,18 +2881,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C3495498", + "display": "Hypertrophic cardiomyopathy 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -3031,9 +2901,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -3042,35 +2912,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "id": "dv-62fab6355932091e78bf4ad7", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "126022" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000383687.3" + "value": "SCV000212630.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb5", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3078,36 +2956,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -3116,18 +2986,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C1838457", - "display": "Fanconi anemia complementation group D1" + "code": "C3495498", + "display": "Hypertrophic cardiomyopathy 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -3136,9 +3006,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -3147,35 +3017,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "id": "dv-62fab6355932091e78bf4aef", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000383699.3" + "value": "SCV002538613.1" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-fd6337f92b2a42dbb2c3410bdfcd9c27", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3183,21 +3061,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -3206,18 +3071,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -3226,17 +3091,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "code": "C3495498", + "display": "Hypertrophic cardiomyopathy 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -3245,99 +3111,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32913054:A:G", - "display": "NC_000013.10:32913054:A:G" - } - ] - } + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "id": "dv-62fab6355932091e78bf4afa", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "14095" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV002059672.1" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C3495498", + "display": "Hypertrophic cardiomyopathy 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -3346,54 +3216,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 32913054 - } + "valueCodeableConcept": { + "text": "no assertion criteria provided" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "id": "dv-62fab6355932091e78bf4ad8", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "14095" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994359, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000035408.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb7", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3401,36 +3271,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -3439,18 +3301,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "CN230736", + "display": "Cardiovascular phenotype", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -3459,9 +3321,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -3470,35 +3332,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "id": "dv-62fab6355932091e78bf4ae5", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000743299.1" + "value": "SCV000318794.5" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb8", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3506,36 +3376,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -3544,18 +3406,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "CN517202", + "display": "not provided", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -3564,9 +3426,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -3575,35 +3437,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "id": "dv-62fab6355932091e78bf4ae4", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000383698.3" + "value": "SCV000208451.14" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb9", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3611,36 +3481,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -3649,18 +3511,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0027672", - "display": "Hereditary cancer-predisposing syndrome" + "code": "CN517202", + "display": "not provided", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -3669,9 +3531,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -3680,35 +3542,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "id": "dv-62fab6355932091e78bf4ae6", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000537315.1" + "value": "SCV001249810.10" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cba", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3716,36 +3586,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -3754,18 +3616,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "CN517202", + "display": "not provided", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -3774,9 +3636,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -3785,35 +3647,43 @@ } } ], - "identifier": [ + "derivedFrom": [ { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "id": "dv-62fab6315932091e78bf2a7d", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "3683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000693637.1" + "value": "SCV002027963.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cbf", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3821,36 +3691,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -3859,18 +3721,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "CN517202", + "display": "not provided", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -3879,46 +3741,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "id": "dv-62fab6355932091e78bf4ad5", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000154035.1" + "value": "SCV001972763.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc1", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3926,36 +3796,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -3964,18 +3826,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "CN517202", + "display": "not provided", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -3984,46 +3846,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "id": "dv-62fab6355932091e78bf4add", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000301764.1" + "value": "SCV000280314.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb0", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4031,36 +3901,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -4069,18 +3931,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "CN517202", + "display": "not provided", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -4089,9 +3951,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -4100,35 +3962,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "id": "dv-62fab6355932091e78bf4ade", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001905911.1" + "value": "SCV002017675.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb1", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4136,36 +4006,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -4174,18 +4036,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "CN517202", - "display": "not provided" + "display": "not provided", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -4194,46 +4056,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" + } + ], + "id": "dv-62fab6355932091e78bf4b1a", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "14095" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000602737.6" + "value": "SCV001959712.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb2", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4241,36 +4111,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6668-3", + "display": "Pathogenic", + "system": "http://loinc.org" } ] } @@ -4279,18 +4141,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "CN517202", + "display": "not provided", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -4299,46 +4161,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" + } + ], + "id": "dv-62fab6315932091e78bf2a77", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "3683" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002026104.2" + "value": "SCV000925133.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc3", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4346,36 +4216,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -4384,18 +4246,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0006142", + "display": "Malignant tumor of breast", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -4404,46 +4266,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17cd9", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000202287.7" + "value": "SCV000592061.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc6", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", - "category": [ - { - "coding": [ + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4451,36 +4321,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -4489,18 +4351,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0006142", + "display": "Malignant tumor of breast", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -4509,17 +4371,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cc7", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -4527,28 +4395,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002097617.1" + "value": "SCV000591909.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb3", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4556,36 +4426,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -4594,18 +4456,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "C0007194", + "display": "Hypertrophic cardiomyopathy", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -4614,46 +4476,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda18", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000778675.1" + "value": "SCV001000422.4" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb4", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4661,36 +4531,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -4699,18 +4561,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0020445", + "display": "Familial hypercholesterolemia", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -4719,46 +4581,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "id": "dv-62fab69e5932091e78c3549d", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "252262" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001951903.1" + "value": "SCV001717062.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cb6", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4766,36 +4636,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -4804,18 +4666,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0027672", - "display": "Hereditary cancer-predisposing syndrome" + "code": "C0020445", + "display": "Familial hypercholesterolemia", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -4824,9 +4686,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -4835,35 +4697,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-904b6ac36b25461ea7a2304093bc6fec" + } + ], + "id": "dv-62fab6a85932091e78c3bb46", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "328058" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000187248.5" + "value": "SCV001717063.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc0", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4871,36 +4741,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -4909,18 +4771,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0346153", - "display": "Familial cancer of breast" + "code": "C0020445", + "display": "Familial hypercholesterolemia", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -4929,46 +4791,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "id": "dv-62fab69e5932091e78c3549c", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "252262" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000541017.1" + "value": "SCV001461329.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc2", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4976,36 +4846,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -5014,18 +4876,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C0027672", + "display": "Hereditary cancer-predisposing syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -5034,9 +4896,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -5045,35 +4907,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15bf4", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000494326.1" + "value": "SCV000537340.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc7", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5081,36 +4951,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -5119,18 +4981,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0006142", - "display": "Malignant tumor of breast" + "code": "C0027672", + "display": "Hereditary cancer-predisposing syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -5139,46 +5001,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15bff", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000591909.2" + "value": "SCV002533822.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc8", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5186,36 +5056,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -5224,18 +5086,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0027672", + "display": "Hereditary cancer-predisposing syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -5244,9 +5106,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -5255,35 +5117,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15c05", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000586951.1" + "value": "SCV000185213.5" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cbb", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5291,36 +5161,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -5329,18 +5191,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0027672", + "display": "Hereditary cancer-predisposing syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -5349,9 +5211,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -5360,35 +5222,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17cd1", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000195985.1" + "value": "SCV002536241.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cbc", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5396,36 +5266,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -5434,18 +5296,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0027672", + "display": "Hereditary cancer-predisposing syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -5454,46 +5316,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17cdb", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000245032.1" + "value": "SCV000212687.4" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cbd", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5501,36 +5371,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -5539,18 +5401,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C0027672", + "display": "Hereditary cancer-predisposing syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -5559,9 +5421,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -5570,35 +5432,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17cdd", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000635377.5" + "value": "SCV000537316.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cbe", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5606,36 +5476,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -5644,18 +5506,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0027672", + "display": "Hereditary cancer-predisposing syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -5664,9 +5526,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -5675,6 +5537,12 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cb6", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -5682,28 +5550,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000167365.11" + "value": "SCV000187248.5" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc4", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5711,36 +5581,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -5749,18 +5611,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0027672", + "display": "Hereditary cancer-predisposing syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -5769,17 +5631,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cb9", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -5787,28 +5655,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000733258.1" + "value": "SCV000537315.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc5", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5816,36 +5686,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -5854,18 +5716,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0346153", + "display": "Familial cancer of breast", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -5874,9 +5736,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -5885,35 +5747,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15bf0", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132779" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000268809.3" + "value": "SCV000541022.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17ccb", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5921,36 +5791,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -5959,18 +5821,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0346153", + "display": "Familial cancer of breast", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -5979,17 +5841,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17cc9", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -5997,28 +5865,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000733283.1" + "value": "SCV000541018.1" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-f61ead8c31904509a974397555d4729d", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6026,21 +5896,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -6049,18 +5906,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -6069,17 +5926,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "code": "C0346153", + "display": "Familial cancer of breast", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -6088,99 +5946,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32915004:G:C", - "display": "NC_000013.10:32915004:G:C" - } - ] - } + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cc0", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132779" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000541017.1" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "G" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -6189,54 +6051,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 32915004 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15bf3", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994199, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001000460.4" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17ccd", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6244,36 +6106,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -6282,18 +6136,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -6302,46 +6156,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15c00", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001958810.1" + "value": "SCV000494320.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17ccf", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6349,36 +6211,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -6387,18 +6241,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -6407,46 +6261,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15c01", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000778699.1" + "value": "SCV002026093.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd2", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6454,36 +6316,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -6492,18 +6346,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -6512,9 +6366,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -6523,35 +6377,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "id": "dv-62fab6705932091e78c186e3", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000743322.1" + "value": "SCV002025816.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd4", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6559,36 +6421,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -6597,18 +6451,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -6617,9 +6471,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -6628,35 +6482,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "id": "dv-62fab6705932091e78c186e7", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000383747.3" + "value": "SCV001000149.4" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd9", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6664,36 +6526,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -6702,18 +6556,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0006142", - "display": "Malignant tumor of breast" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -6722,17 +6576,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17ccc", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -6740,28 +6600,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000592061.2" + "value": "SCV002025800.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cdb", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6769,36 +6631,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -6807,18 +6661,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0027672", - "display": "Hereditary cancer-predisposing syndrome" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -6827,9 +6681,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -6838,6 +6692,12 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17cd7", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -6845,28 +6705,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000212687.4" + "value": "SCV000635514.5" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cdc", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6874,36 +6736,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -6912,18 +6766,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -6932,9 +6786,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -6943,6 +6797,12 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17ce1", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -6950,28 +6810,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000605771.2" + "value": "SCV000494339.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cdd", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6979,36 +6841,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -7017,18 +6871,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0027672", - "display": "Hereditary cancer-predisposing syndrome" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -7037,9 +6891,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -7048,35 +6902,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cb2", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000537316.1" + "value": "SCV002026104.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17ce0", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7084,36 +6946,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -7122,18 +6976,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0677776", + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -7142,9 +6996,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -7153,35 +7007,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cbd", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000154059.1" + "value": "SCV000635377.5" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17ce1", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7189,36 +7051,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -7227,18 +7081,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "display": "Hereditary breast ovarian cancer syndrome", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -7247,9 +7101,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -7258,35 +7112,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cc2", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000494339.1" + "value": "SCV000494326.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17ce2", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7294,36 +7156,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -7332,18 +7186,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -7352,46 +7206,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-0cbf052b7dc2453c83798496893eeb8a" + } + ], + "id": "dv-62fab6a85932091e78c3bb6d", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "328091" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001906399.1" + "value": "SCV000410582.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cc9", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7399,36 +7261,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -7437,18 +7291,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0346153", - "display": "Familial cancer of breast" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -7457,9 +7311,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -7468,35 +7322,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-24497150208846dbbb94cf13157d76d1" + } + ], + "id": "dv-62fab6a85932091e78c3bb84", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "328096" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000541018.1" + "value": "SCV000410587.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17ccc", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7504,36 +7366,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -7542,18 +7396,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -7562,9 +7416,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -7573,35 +7427,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-25751058304a4b40a5254642589509ae" + } + ], + "id": "dv-62fab6a85932091e78c3bb4f", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "328064" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002025800.2" + "value": "SCV000410555.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd3", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7609,36 +7471,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -7647,18 +7501,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -7667,9 +7521,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -7678,35 +7532,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-3bd5a669b6b14313bb6585f4f0249b8e" + } + ], + "id": "dv-62fab6a85932091e78c3bb83", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "328099" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002097618.1" + "value": "SCV000410590.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd5", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7714,36 +7576,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -7752,18 +7606,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -7772,46 +7626,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "id": "dv-62fab69e5932091e78c35499", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "252262" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000245036.1" + "value": "SCV000323005.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cdf", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7819,36 +7681,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -7857,18 +7711,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -7877,9 +7731,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -7888,35 +7742,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "id": "dv-62fab69e5932091e78c3549a", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "252262" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000167382.11" + "value": "SCV000295923.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cca", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7924,36 +7786,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -7962,18 +7816,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -7982,9 +7836,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -7993,35 +7847,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "id": "dv-62fab69e5932091e78c3549e", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "252262" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000202293.7" + "value": "SCV000410543.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd1", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8029,36 +7891,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -8067,18 +7921,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0027672", - "display": "Hereditary cancer-predisposing syndrome" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -8087,9 +7941,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -8098,35 +7952,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "id": "dv-62fab69e5932091e78c354a4", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "252262" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002536241.1" + "value": "SCV001738025.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd6", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8134,36 +7996,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -8172,18 +8026,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -8192,9 +8046,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -8203,35 +8057,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "id": "dv-62fab69e5932091e78c354a5", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "252262" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000602743.6" + "value": "SCV000689775.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cde", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8239,36 +8101,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -8277,18 +8131,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -8297,9 +8151,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -8308,35 +8162,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "id": "dv-62fab69e5932091e78c354ab", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "252262" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000195998.1" + "value": "SCV000987010.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cce", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8344,36 +8206,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -8382,18 +8236,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -8402,9 +8256,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -8413,35 +8267,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-40f05bda5c564d8bb5d775df91b83873" + } + ], + "id": "dv-62fab6a85932091e78c3bb6e", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "328092" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000586969.1" + "value": "SCV000410583.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd0", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8449,36 +8311,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -8487,18 +8341,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C1838457", - "display": "Fanconi anemia complementation group D1" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -8507,9 +8361,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -8518,35 +8372,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-47e65009ae414a218cf7efe34f83c3e0" + } + ], + "id": "dv-62fab6a85932091e78c3bb71", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "328102" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000383746.3" + "value": "SCV000410593.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd7", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8554,36 +8416,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -8592,18 +8446,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -8612,9 +8466,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -8623,35 +8477,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-5459aa2045a740c0af8c14cbc66cd4f2" + } + ], + "id": "dv-62fab6a85932091e78c3bb72", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "328103" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000635514.5" + "value": "SCV000410594.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cd8", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8659,36 +8521,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -8697,18 +8551,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -8717,9 +8571,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -8728,35 +8582,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-57370e44f9884d8cb43661abf73c23c3" + } + ], + "id": "dv-62fab6a85932091e78c3bb55", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "328070" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000693639.1" + "value": "SCV000410561.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66f5932091e78c17cda", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8764,36 +8626,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -8802,18 +8656,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -8822,9 +8676,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -8833,35 +8687,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-7811771c3f3344dca8b4fcf0f9fd84b1" + } + ], + "id": "dv-62fab6a85932091e78c3bb73", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "132780" + "value": "328104" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000301767.1" + "value": "SCV000410595.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e2", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8869,50 +8731,48 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "not provided" + "coding": [ + { + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -8921,46 +8781,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-904b6ac36b25461ea7a2304093bc6fec" + } + ], + "id": "dv-62fab6a85932091e78c3bb47", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" + "value": "328058" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000084509.1" + "value": "SCV000410549.3" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-e2e6891735854abd8abb5a30cc6cc0e0", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8968,21 +8836,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -8991,18 +8846,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -9011,17 +8866,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -9030,99 +8886,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000013.10:32929386:T:C", - "display": "NC_000013.10:32929386:T:C" - } - ] - } + "reference": "Observation/dv-930a27aa386d4cb8bff1e437040afb45" + } + ], + "id": "dv-62fab6a85932091e78c3bb59", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "328072" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000410563.3" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "T" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -9131,54 +8991,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 32929386 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.994876, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "reference": "Observation/dv-9ad6695f56dd4d82afb319c8331d3a6d" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186f5", + ], + "id": "dv-62fab6a85932091e78c3bb85", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "328095" + }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000410586.3" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -9186,36 +9046,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -9224,18 +9076,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -9244,9 +9096,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -9255,35 +9107,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-a4bc1ce389c943248c967f087971ba88" + } + ], + "id": "dv-62fab6a85932091e78c3bb75", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" + "value": "328106" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001139178.1" + "value": "SCV000410597.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e0", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -9291,36 +9151,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -9329,18 +9181,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -9349,46 +9201,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-ae2c1cd27dd44fb79b1b949e56ae7833" + } + ], + "id": "dv-62fab6a85932091e78c3bb6a", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" + "value": "328086" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001930871.1" + "value": "SCV000410577.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e1", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -9396,36 +9256,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -9434,18 +9286,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -9454,46 +9306,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-ec3a667068394825be063d587250d6e2" + } + ], + "id": "dv-62fab6a25932091e78c37a93", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" + "value": "265910" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001550303.1" + "value": "SCV000323020.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e5", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -9501,36 +9361,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA26333-7", - "display": "Uncertain significance" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -9539,18 +9391,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C1527349", - "display": "Ductal breast carcinoma" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -9559,46 +9411,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-ec3a667068394825be063d587250d6e2" + } + ], + "id": "dv-62fab6a25932091e78c37a94", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" + "value": "265910" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000258682.1" + "value": "SCV001738049.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e6", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -9606,36 +9466,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -9644,18 +9496,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -9664,46 +9516,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-ec3a667068394825be063d587250d6e2" + } + ], + "id": "dv-62fab6a25932091e78c37a95", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" + "value": "265910" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001906256.1" + "value": "SCV000410546.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186ec", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -9711,36 +9571,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -9749,18 +9601,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -9769,9 +9621,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -9780,35 +9632,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-ec3a667068394825be063d587250d6e2" + } + ], + "id": "dv-62fab6a25932091e78c37a96", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" + "value": "265910" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000202300.7" + "value": "SCV000987011.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186f3", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", - "category": [ + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -9816,36 +9676,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -9854,18 +9706,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C0745103", + "display": "Hypercholesterolemia, familial, 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -9874,46 +9726,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "id": "dv-62fab69e5932091e78c354a1", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" + "value": "252262" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002097591.1" + "value": "SCV000606617.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e4", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -9921,36 +9781,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -9959,18 +9811,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "C0878544", + "display": "Cardiomyopathy", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -9979,9 +9831,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -9990,35 +9842,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda16", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000602752.5" + "value": "SCV000902546.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e7", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -10026,36 +9886,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -10064,18 +9916,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C0878544", + "display": "Cardiomyopathy", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -10084,46 +9936,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda12", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001000149.4" + "value": "SCV000564487.4" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e9", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -10131,36 +9991,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -10169,18 +10021,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C1834481", + "display": "Dilated cardiomyopathy 1S", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -10189,46 +10041,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda0a", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001979638.1" + "value": "SCV000386095.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186ea", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -10236,36 +10096,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -10274,18 +10126,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C1838457", + "display": "Fanconi anemia complementation group D1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -10294,9 +10146,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -10305,35 +10157,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" + } + ], + "id": "dv-62fab66c5932091e78c15a83", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" + "value": "125927" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000268811.3" + "value": "SCV000383815.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e3", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -10341,36 +10201,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -10379,18 +10231,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0677776", - "display": "Hereditary breast ovarian cancer syndrome" + "code": "C1838457", + "display": "Fanconi anemia complementation group D1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -10399,9 +10251,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -10410,35 +10262,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15bfb", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002025816.2" + "value": "SCV000383688.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6705932091e78c186e8", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -10446,36 +10306,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -10484,18 +10336,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C1838457", + "display": "Fanconi anemia complementation group D1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -10504,46 +10356,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17cd0", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "133738" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001744232.3" + "value": "SCV000383746.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15a82", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -10551,36 +10411,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -10589,18 +10441,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "code": "C1838457", + "display": "Fanconi anemia complementation group D1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -10609,9 +10461,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -10620,35 +10472,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cb5", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "125927" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000383816.3" + "value": "SCV000383699.3" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-b49765544a4f4ffdb9856882d59ea768", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -10656,21 +10516,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - 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- ] - } + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda09", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "42942" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000386099.3" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -10819,38 +10671,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 32973011 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15a84", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" + } + ], + "id": "dv-62fab66c5932091e78c15a82", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + 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"https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -10916,17 +10776,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" + } + ], + "id": "dv-62fab66c5932091e78c15a85", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -10934,28 +10800,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000145775.1" + "value": "SCV000743532.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15a86", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -10963,36 +10831,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -11001,18 +10861,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -11021,46 +10881,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15bed", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "125927" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001906326.1" + "value": "SCV000154051.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15a8b", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -11068,36 +10936,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -11106,18 +10966,18 @@ "code": { "coding": [ { - "system": 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+ "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000245315.1" + "value": "SCV000195977.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15a87", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -11173,36 +11041,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -11211,18 +11071,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -11231,46 +11091,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15c03", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "125927" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001548650.1" + "value": "SCV000383687.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15a89", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -11278,36 +11146,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -11316,18 +11176,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -11336,9 +11196,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -11347,35 +11207,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15c04", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "125927" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000883471.4" + "value": "SCV000744444.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15a88", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -11383,36 +11251,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -11421,18 +11281,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -11441,9 +11301,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -11452,35 +11312,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15c08", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "125927" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": 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"reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -11526,18 +11386,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C1838457", - "display": "Fanconi anemia complementation group D1" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -11546,9 +11406,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -11557,35 +11417,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "id": "dv-62fab6705932091e78c186f3", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "125927" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000383815.3" + "value": "SCV002097591.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab66c5932091e78c15a85", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -11593,36 +11461,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -11631,18 +11491,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "C2675520", - "display": "Breast-ovarian cancer, familial, susceptibility to, 2" + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -11651,9 +11511,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -11662,35 +11522,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "id": "dv-62fab6705932091e78c186f5", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "125927" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000743532.1" + "value": "SCV001139178.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda01", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -11698,36 +11566,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -11736,18 +11596,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -11756,9 +11616,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -11767,35 +11627,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17cd2", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000170522.11" + "value": "SCV000743322.1" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -11803,21 +11671,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -11826,18 +11681,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -11846,17 +11701,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -11865,99 +11721,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23892887:A:G", - "display": "NC_000014.8:23892887:A:G" - } - ] - } + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17cd3", + "identifier": [ + { + "system": 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"http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -11966,54 +11826,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 23892887 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17cd4", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.308092, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000383747.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda04", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -12021,36 +11881,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -12059,18 +11911,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4552004", - "display": "MYH7-related skeletal myopathy" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -12079,9 +11931,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -12090,35 +11942,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17cde", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000386097.3" + "value": "SCV000195998.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda06", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -12126,36 +11986,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -12164,18 +12016,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -12184,9 +12036,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -12195,35 +12047,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17ce0", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000151919.1" + "value": "SCV000154059.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda09", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -12231,36 +12091,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -12269,18 +12121,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C1842160", - "display": "Myosin storage myopathy" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -12289,9 +12141,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -12300,35 +12152,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cb7", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000386099.3" + "value": "SCV000743299.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda0a", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -12336,36 +12196,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -12374,18 +12226,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C1834481", - "display": "Dilated cardiomyopathy 1S" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -12394,9 +12246,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -12405,35 +12257,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cb8", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000386095.3" + "value": "SCV000383698.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda0c", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -12441,36 +12301,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -12479,18 +12331,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3495498", - "display": "Hypertrophic cardiomyopathy 1" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -12499,9 +12351,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -12510,35 +12362,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cbb", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000386098.3" + "value": "SCV000195985.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda17", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -12546,36 +12406,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA26333-7", - "display": "Uncertain significance" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -12584,18 +12436,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -12604,46 +12456,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cbf", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001551199.1" + "value": "SCV000154035.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda19", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -12651,36 +12511,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -12689,18 +12541,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -12709,46 +12561,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cc6", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001920413.1" + "value": "SCV002097617.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda02", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -12756,36 +12616,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -12794,18 +12646,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -12814,9 +12666,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -12825,35 +12677,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15beb", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001930264.1" + "value": "SCV000189304.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda08", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -12861,36 +12721,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -12899,18 +12751,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -12919,9 +12771,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -12930,35 +12782,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15bef", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001951128.1" + "value": "SCV000146298.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda0f", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -12966,36 +12826,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], - "component": [ + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -13004,18 +12856,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -13024,9 +12876,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -13035,35 +12887,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15bf7", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001975767.1" + "value": "SCV000733249.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda14", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -13071,36 +12931,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -13109,18 +12961,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -13129,46 +12981,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17ccb", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000303219.1" + "value": "SCV000733283.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda0e", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -13176,36 +13036,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -13214,18 +13066,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -13234,46 +13086,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cc4", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001433073.1" + "value": "SCV000733258.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda12", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -13281,36 +13141,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -13319,18 +13171,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0878544", - "display": "Cardiomyopathy" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -13339,9 +13191,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -13350,35 +13202,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" + } + ], + "id": "dv-62fab66c5932091e78c15a8b", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" + "value": "125927" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000564487.4" + "value": "SCV000245315.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda15", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -13386,36 +13246,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -13424,18 +13276,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -13444,46 +13296,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15bee", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000059486.5" + "value": "SCV000245028.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda18", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -13491,36 +13351,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -13529,18 +13381,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0007194", - "display": "Hypertrophic cardiomyopathy" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -13549,46 +13401,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17cd5", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001000422.4" + "value": "SCV000245036.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda03", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -13596,36 +13456,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -13634,18 +13486,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C4021133", - "display": "Left ventricular noncompaction cardiomyopathy" + "code": "C2675520", + "display": "Breast-ovarian cancer, familial, susceptibility to, 2", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -13654,83 +13506,83 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "reviewed by expert panel" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cbc", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "42942" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000386100.2" + "value": "SCV000245032.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda07", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } ] } ], "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -13739,18 +13591,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN169374", - "display": "not specified" + "code": "C3495498", + "display": "Hypertrophic cardiomyopathy 1", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -13759,17 +13611,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda0c", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -13777,28 +13635,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001742640.3" + "value": "SCV000386098.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda0d", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -13806,36 +13666,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -13844,18 +13696,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN230736", - "display": "Cardiovascular phenotype" + "code": "C4021133", + "display": "Left ventricular noncompaction cardiomyopathy", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -13864,9 +13716,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -13875,6 +13727,12 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda03", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -13882,28 +13740,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000317659.5" + "value": "SCV000386100.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6455932091e78bfda16", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -13911,36 +13771,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -13949,18 +13801,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0878544", - "display": "Cardiomyopathy" + "code": "C4552004", + "display": "MYH7-related skeletal myopathy", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -13969,9 +13821,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -13980,6 +13832,12 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda04", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", @@ -13987,28 +13845,30 @@ }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000902546.1" + "value": "SCV000386097.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4ad5", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -14016,36 +13876,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -14054,18 +13906,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -14074,46 +13926,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "id": "dv-62fab69e5932091e78c3549f", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" + "value": "252262" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001972763.1" + "value": "SCV000524334.4" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -14121,21 +13981,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -14144,18 +13991,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -14164,17 +14011,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000014.8" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -14183,38 +14031,83 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "id": "dv-62fab69e5932091e78c354a0", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "252262" }, + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000304691.1" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" + } + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000014.8:23895022:G:A", - "display": "NC_000014.8:23895022:G:A" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -14223,115 +14116,74 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 23895022 - } - } + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "id": "dv-62fab69e5932091e78c354a2", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "252262" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 1.1942e-05, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000711400.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4ad7", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -14339,36 +14191,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -14377,18 +14221,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3495498", - "display": "Hypertrophic cardiomyopathy 1" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -14397,9 +14241,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -14408,35 +14252,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda01", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000212630.1" + "value": "SCV000170522.11" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4ae5", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -14444,36 +14296,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -14482,18 +14326,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN230736", - "display": "Cardiovascular phenotype" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -14502,9 +14346,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -14513,35 +14357,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda06", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000318794.5" + "value": "SCV000151919.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4ae6", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -14549,36 +14401,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -14587,18 +14431,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -14607,9 +14451,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -14618,35 +14462,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda0e", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001249810.10" + "value": "SCV001433073.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4aea", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -14654,36 +14506,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -14692,18 +14536,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0007194", - "display": "Hypertrophic cardiomyopathy" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -14712,46 +14556,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda14", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000564425.4" + "value": "SCV000303219.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4aef", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -14759,36 +14611,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -14797,18 +14641,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3495498", - "display": "Hypertrophic cardiomyopathy 1" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -14817,9 +14661,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -14828,35 +14672,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda15", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002538613.1" + "value": "SCV000059486.5" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4afb", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -14864,36 +14716,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA26332-9", - "display": "Likely pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -14902,18 +14746,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -14922,46 +14766,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" + } + ], + "id": "dv-62fab66c5932091e78c15a88", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" + "value": "125927" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001739623.3" + "value": "SCV000693649.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4ad6", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -14969,36 +14821,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA26332-9", - "display": "Likely pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -15007,18 +14851,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0949658", - "display": "Primary familial hypertrophic cardiomyopathy" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -15027,46 +14871,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15bf1", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000188798.1" + "value": "SCV000202285.7" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4add", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -15074,36 +14926,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -15112,18 +14956,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -15132,46 +14976,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15bf6", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000280314.1" + "value": "SCV000301763.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4ade", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -15179,36 +15031,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -15217,18 +15061,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -15237,46 +15081,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15bf8", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002017675.1" + "value": "SCV000538459.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4adf", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -15284,36 +15136,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -15322,18 +15166,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0007194", - "display": "Hypertrophic cardiomyopathy" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -15342,9 +15186,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -15353,35 +15197,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15bf9", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000546190.6" + "value": "SCV000693636.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4b17", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -15389,36 +15241,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -15427,18 +15271,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0878544", - "display": "Cardiomyopathy" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -15447,9 +15291,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -15458,35 +15302,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15bfe", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001352585.2" + "value": "SCV000586945.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4b1a", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -15494,36 +15346,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -15532,18 +15376,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -15552,46 +15396,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "id": "dv-62fab6705932091e78c186ea", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001959712.2" + "value": "SCV000268811.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4ae3", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -15599,36 +15451,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -15637,18 +15481,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0007194", - "display": "Hypertrophic cardiomyopathy" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -15657,9 +15501,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -15668,35 +15512,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "id": "dv-62fab6705932091e78c186ec", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000059423.7" + "value": "SCV000202300.7" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4ad8", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -15704,36 +15556,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -15742,18 +15586,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3495498", - "display": "Hypertrophic cardiomyopathy 1" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -15762,46 +15606,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17cca", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000035408.2" + "value": "SCV000202293.7" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4ae4", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -15809,36 +15661,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -15847,18 +15691,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -15867,9 +15711,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -15878,35 +15722,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17cce", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000208451.14" + "value": "SCV000586969.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6355932091e78bf4afa", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -15914,36 +15766,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0e81b678f2aa4151b1cba965d0fbaab7" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -15952,18 +15796,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C3495498", - "display": "Hypertrophic cardiomyopathy 1" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -15972,9 +15816,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -15983,35 +15827,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17cd8", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "14095" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002059672.1" + "value": "SCV000693639.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a75", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -16019,36 +15871,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -16057,18 +15901,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -16077,9 +15921,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -16088,35 +15932,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17cda", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000294463.2" + "value": "SCV000301767.1" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-46597e63d927405d8818e0867d0e521c", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -16124,21 +15976,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -16147,18 +15986,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -16167,17 +16006,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -16186,99 +16026,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17cdc", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11210927:C:T", - "display": "NC_000019.9:11210927:C:T" - } - ] - } - }, + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000605771.2" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "C" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -16287,54 +16131,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 11210927 - } + "valueCodeableConcept": { + "text": "criteria provided, single submitter" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17cdf", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "132780" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 7.96318e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV000167382.11" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a79", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -16342,36 +16186,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -16380,18 +16216,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -16400,46 +16236,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "reviewed by expert panel" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cba", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002506409.1" + "value": "SCV000693637.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a7b", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -16447,36 +16291,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -16485,18 +16321,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -16505,9 +16341,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -16516,35 +16352,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cbe", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000588484.1" + "value": "SCV000167365.11" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a7c", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -16552,36 +16396,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -16590,18 +16426,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -16610,46 +16446,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cc1", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000606015.1" + "value": "SCV000301764.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a7e", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -16657,36 +16501,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -16695,18 +16531,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -16715,9 +16551,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -16726,35 +16562,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cc3", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000987040.1" + "value": "SCV000202287.7" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a76", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -16762,36 +16606,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -16800,18 +16636,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -16820,46 +16656,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cc5", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002017112.1" + "value": "SCV000268809.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a7d", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -16867,36 +16711,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -16905,18 +16741,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -16925,9 +16761,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -16936,35 +16772,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cc8", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002027963.1" + "value": "SCV000586951.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a7f", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -16972,36 +16816,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -17010,18 +16846,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -17030,46 +16866,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "id": "dv-62fab69e5932091e78c3549b", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "252262" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000503101.1" + "value": "SCV001926076.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a71", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -17077,36 +16921,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -17115,18 +16951,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -17135,46 +16971,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "id": "dv-62fab69e5932091e78c354a3", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "252262" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000544678.5" + "value": "SCV001740479.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a78", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -17182,36 +17026,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -17220,18 +17056,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -17240,46 +17076,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda02", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000583630.1" + "value": "SCV001930264.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a7a", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -17287,36 +17131,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -17325,18 +17161,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -17345,46 +17181,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda07", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000607415.1" + "value": "SCV001742640.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a80", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -17392,36 +17236,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -17430,18 +17266,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -17450,9 +17286,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -17461,35 +17297,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda08", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002086359.1" + "value": "SCV001951128.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a6e", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -17497,36 +17341,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -17535,18 +17371,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -17555,46 +17391,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda0f", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001653581.1" + "value": "SCV001975767.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a77", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -17602,36 +17446,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -17640,18 +17476,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -17660,9 +17496,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -17671,35 +17507,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda19", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000925133.1" + "value": "SCV001920413.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6315932091e78bf2a82", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -17707,36 +17551,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-46597e63d927405d8818e0867d0e521c" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6668-3", - "display": "Pathogenic" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -17745,18 +17581,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -17765,9 +17601,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -17776,35 +17612,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" + } + ], + "id": "dv-62fab66c5932091e78c15a86", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "3683" + "value": "125927" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000024033.3" + "value": "SCV001906326.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c3549a", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -17812,36 +17656,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -17850,18 +17686,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -17870,46 +17706,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" + } + ], + "id": "dv-62fab66c5932091e78c15a87", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "125927" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000295923.2" + "value": "SCV001548650.1" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-3f58c03ccc244f01820bf9445e076d69", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -17917,21 +17761,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -17940,18 +17771,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -17960,17 +17791,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -17979,99 +17811,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] + "text": "no assertion criteria provided" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11233940:A:G", - "display": "NC_000019.9:11233940:A:G" - } - ] - } - }, + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15bf5", + "identifier": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, { - "code": { + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001551831.1" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" + } + ] + }, + "component": [ + { + "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -18080,54 +17916,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 11233940 - } + "valueCodeableConcept": { + "text": "no assertion criteria provided" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15bfc", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "126022" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 0.781146, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", + "value": "SCV001906228.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c3549c", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -18135,36 +17971,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -18173,18 +18001,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -18193,9 +18021,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -18204,35 +18032,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15c02", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001461329.1" + "value": "SCV001953719.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c3549f", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -18240,36 +18076,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -18278,18 +18106,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "CN169374", - "display": "not specified" + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -18298,46 +18126,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "id": "dv-62fab6705932091e78c186e0", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000524334.4" + "value": "SCV001930871.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c354a3", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -18345,36 +18181,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -18383,18 +18211,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "CN169374", - "display": "not specified" + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -18403,9 +18231,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -18414,35 +18242,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "id": "dv-62fab6705932091e78c186e1", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001740479.3" + "value": "SCV001550303.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c354a5", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -18450,36 +18286,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -18488,18 +18316,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -18508,46 +18336,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "id": "dv-62fab6705932091e78c186e6", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000689775.1" + "value": "SCV001906256.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c35498", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -18555,36 +18391,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -18593,18 +18421,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "CN517202", - "display": "not provided" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -18613,46 +18441,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], - "identifier": [ + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "id": "dv-62fab6705932091e78c186e8", + "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV002049746.2" + "value": "SCV001744232.3" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c3549b", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -18660,36 +18496,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -18698,18 +18526,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "CN169374", - "display": "not specified" + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -18718,9 +18546,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -18729,35 +18557,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "id": "dv-62fab6705932091e78c186e9", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001926076.1" + "value": "SCV001979638.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c3549d", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -18765,36 +18601,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -18803,18 +18631,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -18823,46 +18651,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17ccd", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001717062.2" + "value": "SCV001958810.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c3549e", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -18870,36 +18706,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -18908,18 +18736,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -18928,46 +18756,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17ce2", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410543.3" + "value": "SCV001906399.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c354a0", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -18975,36 +18811,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -19013,18 +18841,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "CN169374", - "display": "not specified" + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -19033,46 +18861,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cb0", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000304691.1" + "value": "SCV001905911.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c354a2", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -19080,36 +18916,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -19118,18 +18946,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", "code": "CN169374", - "display": "not specified" + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -19138,46 +18966,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cb4", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000711400.2" + "value": "SCV001951903.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c354ab", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -19185,36 +19021,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -19223,18 +19051,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN230736", + "display": "Cardiovascular phenotype", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -19243,9 +19071,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -19254,35 +19082,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-45d90d04eaf548d5b98b6528f6fdc045" + } + ], + "id": "dv-62fab6455932091e78bfda0d", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "42942" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000987010.1" + "value": "SCV000317659.5" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c354a4", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -19290,36 +19126,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -19328,18 +19156,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN517202", + "display": "not provided", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -19348,9 +19176,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -19359,35 +19187,43 @@ } } ], - "identifier": [ + "derivedFrom": [ + { + "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" + } + ], + "id": "dv-62fab69e5932091e78c35498", + "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", "value": "252262" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001738025.1" + "value": "SCV002049746.2" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c35499", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -19395,36 +19231,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -19433,18 +19261,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN517202", + "display": "not provided", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -19453,9 +19281,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -19464,35 +19292,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-b49765544a4f4ffdb9856882d59ea768" + } + ], + "id": "dv-62fab66c5932091e78c15a89", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "125927" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000323005.1" + "value": "SCV000883471.4" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab69e5932091e78c354a1", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -19500,36 +19336,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-3f58c03ccc244f01820bf9445e076d69" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -19538,18 +19366,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN517202", + "display": "not provided", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -19558,46 +19386,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "no assertion criteria provided" + "text": "criteria provided, single submitter" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15bfd", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "252262" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000606617.1" + "value": "SCV000602744.6" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a25932091e78c37a93", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -19605,36 +19441,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-ec3a667068394825be063d587250d6e2" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -19643,18 +19471,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN517202", + "display": "not provided", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -19663,9 +19491,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -19674,35 +19502,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "id": "dv-62fab6705932091e78c186e4", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "265910" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000323020.1" + "value": "SCV000602752.5" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-ec3a667068394825be063d587250d6e2", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -19710,21 +19546,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -19733,18 +19556,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "53037-8", + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -19753,17 +19576,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "CN517202", + "display": "not provided", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -19772,99 +19596,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] + "text": "criteria provided, single submitter" } - }, + } + ], + "derivedFrom": [ { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242043:G:A", - "display": "NC_000019.9:11242043:G:A" - } - ] - } + "reference": "Observation/dv-ec3a667068394825be063d587250d6e2" + } + ], + "id": "dv-62fab6a25932091e78c37a92", + "identifier": [ + { + "system": "http://www.ncbi.nlm.nih.gov/clinvar", + "value": "265910" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", 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"http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "LA6675-8", + "display": "Benign", + "system": "http://loinc.org" } ] - }, - "valueString": "A" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81259-4", + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "CN517202", + "display": "not provided", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -19873,54 +19701,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 11242043 - } + "valueCodeableConcept": { + "text": "criteria provided, single 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"http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-ec3a667068394825be063d587250d6e2" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -20071,18 +19891,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN517202", + "display": "not provided", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -20091,46 +19911,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-c2f729c9baee4e9290dfc7dae09d497f" + } + ], + "id": "dv-62fab66c5932091e78c15bf2", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "265910" + "value": "126022" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001738049.1" + "value": "SCV000778666.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a25932091e78c37a95", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -20138,36 +19966,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-ec3a667068394825be063d587250d6e2" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": 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"http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-f61ead8c31904509a974397555d4729d" + } + ], + "id": "dv-62fab66f5932091e78c17ccf", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "265910" + "value": "132780" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410546.3" + "value": "SCV000778699.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a25932091e78c37a96", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -20243,36 +20071,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-ec3a667068394825be063d587250d6e2" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6675-8", - "display": "Benign" + "display": "Benign", + "system": "http://loinc.org" } ] } @@ -20281,18 +20101,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "CN517202", + "display": "not provided", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -20301,46 +20121,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion criteria provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-fd6337f92b2a42dbb2c3410bdfcd9c27" + } + ], + "id": "dv-62fab66f5932091e78c17cb3", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "265910" + "value": "132779" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000987011.1" + "value": "SCV000778675.1" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb46", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -20348,56 +20176,42 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "diagnostic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-904b6ac36b25461ea7a2304093bc6fec" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "53037-8", - "display": "Genetic variation clinical significance" + "display": "Genetic variation clinical significance", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "text": "not provided" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "81259-4", - "display": "predicted phenotype" + "display": "predicted phenotype", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0020445", - "display": "Familial hypercholesterolemia" + "code": "CN169374", + "display": "not specified", + "system": "https://www.ncbi.nlm.nih.gov/medgen" } ] } @@ -20406,46 +20220,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "text": "no assertion provided" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-e2e6891735854abd8abb5a30cc6cc0e0" + } + ], + "id": "dv-62fab6705932091e78c186e2", "identifier": [ { "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328058" + "value": "133738" }, { "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV001717063.2" + "value": "SCV000084509.1" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-904b6ac36b25461ea7a2304093bc6fec", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -20453,21 +20275,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -20476,18 +20286,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -20496,17 +20306,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000013.10", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -20515,18 +20325,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6705-3", - "display": "homozygous" + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -20535,135 +20345,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "A" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242306:G:C", - "display": "NC_000019.9:11242306:G:C" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "NC_000013.10:32973011:A:C", + "display": "NC_000013.10:32973011:A:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] - }, - "valueString": "G" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueRange": { + "low": { + "value": 32973011 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": 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"coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328064" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410555.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-25751058304a4b40a5254642589509ae", + "id": "dv-0e81b678f2aa4151b1cba965d0fbaab7", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -20986,21 +21567,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -21009,18 +21578,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -21029,17 +21598,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000014.8", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -21048,18 +21617,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -21068,18 +21637,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "A" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, + { + "code": { + "coding": [ + { "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242495:G:A", - "display": "NC_000019.9:11242495:G:A" + "code": "NC_000014.8:23892887:A:G", + "display": "NC_000014.8:23892887:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -21088,99 +21681,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 23892887 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.308092 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11242495 - } } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb4e", + ], + "id": "dv-45d90d04eaf548d5b98b6528f6fdc045", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -21188,36 +21785,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-25751058304a4b40a5254642589509ae" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA26334-5", - "display": "Likely benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -21226,18 +21816,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -21246,151 +21835,167 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328064" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000987015.1" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb56", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "A" + }, { - "reference": "Observation/dv-57370e44f9884d8cb43661abf73c23c3" - } - ], - "component": [ + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA26334-5", - "display": "Likely benign" + "code": "NC_000019.9:11233940:A:G", + "display": "NC_000019.9:11233940:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] + }, + "valueRange": { + "low": { + "value": 11233940 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } + }, + { + "code": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.781146 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328070" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000987013.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-57370e44f9884d8cb43661abf73c23c3", + "id": "dv-3f58c03ccc244f01820bf9445e076d69", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -21398,21 +22003,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -21421,18 +22014,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -21441,17 +22034,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -21460,18 +22053,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6705-3", - "display": "homozygous" + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -21480,18 +22073,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "C" + }, + { + "code": { + "coding": [ + { "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242657:T:C", - "display": "NC_000019.9:11242657:T:C" + "code": "NC_000019.9:11242306:G:C", + "display": "NC_000019.9:11242306:G:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -21500,99 +22117,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 11242306 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.818994 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11242657 - } } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb55", + ], + "id": "dv-904b6ac36b25461ea7a2304093bc6fec", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -21600,36 +22221,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-57370e44f9884d8cb43661abf73c23c3" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -21638,18 +22252,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -21658,83 +22271,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328070" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410561.3" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb58", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "T" + }, { - "reference": "Observation/dv-930a27aa386d4cb8bff1e437040afb45" - } - ], - "component": [ + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "C" + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA26334-5", - "display": "Likely benign" + "code": "NC_000019.9:11242657:T:C", + "display": "NC_000019.9:11242657:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -21743,66 +22335,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 11242657 + } + } + }, + { + "code": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328072" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000987014.1" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-930a27aa386d4cb8bff1e437040afb45", + "id": "dv-57370e44f9884d8cb43661abf73c23c3", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -21810,21 +22423,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -21833,18 +22434,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -21853,17 +22454,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -21872,18 +22473,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -21892,119 +22493,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "T" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242764:A:G", - "display": "NC_000019.9:11242764:A:G" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243253:T:C", + "display": "NC_000019.9:11243253:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueRange": { + "low": { + "value": 11243253 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11242764 - } } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb59", + ], + "id": "dv-0cbf052b7dc2453c83798496893eeb8a", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -22012,36 +22625,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-930a27aa386d4cb8bff1e437040afb45" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -22050,18 +22656,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -22070,83 +22675,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328072" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410563.3" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb6a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "A" + }, { - "reference": "Observation/dv-ae2c1cd27dd44fb79b1b949e56ae7833" - } - ], - "component": [ + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "NC_000019.9:11242764:A:G", + "display": "NC_000019.9:11242764:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -22155,66 +22739,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 11242764 + } + } + }, + { + "code": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328086" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410577.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-ae2c1cd27dd44fb79b1b949e56ae7833", + ], + "id": "dv-930a27aa386d4cb8bff1e437040afb45", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -22222,21 +22827,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -22245,18 +22838,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -22265,17 +22858,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -22284,18 +22877,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -22304,119 +22897,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "A" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243159:G:A", - "display": "NC_000019.9:11243159:G:A" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243444:A:G", + "display": "NC_000019.9:11243444:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueRange": { + "low": { + "value": 11243444 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243159 - } } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb6b", + ], + "id": "dv-47e65009ae414a218cf7efe34f83c3e0", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -22424,36 +23029,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-d5e6a6a584a44454901740ac1d9c4b1f" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA26334-5", - "display": "Likely benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -22462,18 +23060,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -22482,68 +23079,161 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ + }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328089" + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "C" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410580.2" + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "A" + }, + { + "code": { + "coding": [ + { + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243331:C:A", + "display": "NC_000019.9:11243331:C:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" + } + ] + }, + "valueRange": { + "low": { + "value": 11243331 + } + } + }, + { + "code": { + "coding": [ + { + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" + } + ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] + } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-d5e6a6a584a44454901740ac1d9c4b1f", + ], + "id": "dv-24497150208846dbbb94cf13157d76d1", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, "subject": { "reference": "Patient/HG00403" }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -22552,18 +23242,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -22572,17 +23262,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -22591,99 +23281,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243223:CTACTA:CTA", - "display": "NC_000019.9:11243223:CTACTA:CTA" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "TCTA" + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.9:11243327:C:G", + "display": "NC_000019.9:11243327:C:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -22692,143 +23345,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 11243222 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb6d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "value": 11243327 } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0cbf052b7dc2453c83798496893eeb8a" - } - ], - "component": [ + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328091" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410582.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-0cbf052b7dc2453c83798496893eeb8a", + "id": "dv-9ad6695f56dd4d82afb319c8331d3a6d", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -22836,21 +23433,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -22859,18 +23444,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -22879,17 +23464,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -22898,78 +23483,29 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243253:T:C", - "display": "NC_000019.9:11243253:T:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -22979,95 +23515,30 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 11243253 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb6e", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-40f05bda5c564d8bb5d775df91b83873" - } - ], - "component": [ + "valueString": "T" + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "NC_000019.9:11210927:C:T", + "display": "NC_000019.9:11210927:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -23076,66 +23547,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 11210927 + } + } + }, + { + "code": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 7.96318e-06 } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328092" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410583.3" + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] + } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-40f05bda5c564d8bb5d775df91b83873", + ], + "id": "dv-46597e63d927405d8818e0867d0e521c", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -23143,21 +23651,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -23166,18 +23662,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -23186,17 +23682,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -23205,66 +23701,29 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243259:C:T", - "display": "NC_000019.9:11243259:C:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -23274,9 +23733,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, @@ -23286,18 +23745,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.9:11243259:C:T", + "display": "NC_000019.9:11243259:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -23306,9 +23765,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, @@ -23317,132 +23776,76 @@ "value": 11243259 } } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb85", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-9ad6695f56dd4d82afb319c8331d3a6d" - } - ], - "component": [ + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328095" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410586.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-9ad6695f56dd4d82afb319c8331d3a6d", + "id": "dv-40f05bda5c564d8bb5d775df91b83873", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -23450,21 +23853,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -23473,18 +23864,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -23493,57 +23884,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243327:C:G", - "display": "NC_000019.9:11243327:C:G" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -23552,26 +23903,29 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -23581,30 +23935,30 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.9:11243734:C:T", + "display": "NC_000019.9:11243734:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -23613,143 +23967,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 11243327 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb84", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "value": 11243734 } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-24497150208846dbbb94cf13157d76d1" - } - ], - "component": [ + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328096" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410587.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-24497150208846dbbb94cf13157d76d1", + "id": "dv-a4bc1ce389c943248c967f087971ba88", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -23757,21 +24055,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -23780,18 +24066,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -23800,17 +24086,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -23819,78 +24105,41 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243331:C:A", - "display": "NC_000019.9:11243331:C:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, @@ -23900,18 +24149,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.9:11242043:G:A", + "display": "NC_000019.9:11242043:G:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -23920,143 +24169,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 11243331 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb83", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "value": 11242043 } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-3bd5a669b6b14313bb6585f4f0249b8e" - } - ], - "component": [ + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.243375 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328099" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410590.3" - } - ] + "id": "dv-ec3a667068394825be063d587250d6e2", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } }, { "name": "variant", "resource": { - "resourceType": "Observation", - "id": "dv-3bd5a669b6b14313bb6585f4f0249b8e", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -24064,21 +24273,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -24087,18 +24284,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -24107,17 +24304,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -24126,18 +24323,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -24146,119 +24343,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "G" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243367:T:C", - "display": "NC_000019.9:11243367:T:C" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11242495:G:A", + "display": "NC_000019.9:11242495:G:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueRange": { + "low": { + "value": 11242495 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243367 - } } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb71", + ], + "id": "dv-25751058304a4b40a5254642589509ae", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -24266,36 +24475,29 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-47e65009ae414a218cf7efe34f83c3e0" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -24304,18 +24506,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -24324,46 +24525,151 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" + "coding": [ + { + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" + } + ] } - } - ], - "identifier": [ + }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328102" + "code": { + "coding": [ + { + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" }, { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410593.3" + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "A" + }, + { + "code": { + "coding": [ + { + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243159:G:A", + "display": "NC_000019.9:11243159:G:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" + } + ] + }, + "valueRange": { + "low": { + "value": 11243159 + } + } + }, + { + "code": { + "coding": [ + { + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" + } + ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] + } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-47e65009ae414a218cf7efe34f83c3e0", + ], + "id": "dv-ae2c1cd27dd44fb79b1b949e56ae7833", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -24371,60 +24677,29 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" - } - ] - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6683-2", - "display": "germline" - } - ] + "display": "Genetic variant assessment", + "system": "http://loinc.org" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "LA6683-2", + "display": "germline", + "system": "http://loinc.org" } ] } @@ -24433,18 +24708,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53034-5", - "display": "Allelic state" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -24453,79 +24727,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "53034-5", + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243444:A:G", - "display": "NC_000019.9:11243444:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.9:11243591:G:T", + "display": "NC_000019.9:11243591:G:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -24534,143 +24791,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 11243444 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb72", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "value": 11243591 } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-5459aa2045a740c0af8c14cbc66cd4f2" - } - ], - "component": [ + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328103" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410594.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-5459aa2045a740c0af8c14cbc66cd4f2", + "id": "dv-7811771c3f3344dca8b4fcf0f9fd84b1", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -24678,21 +24879,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -24701,18 +24890,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -24721,17 +24910,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -24740,38 +24929,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243501:T:C", - "display": "NC_000019.9:11243501:T:C" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -24780,26 +24949,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -24809,9 +24961,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, @@ -24821,18 +24973,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.9:11243367:T:C", + "display": "NC_000019.9:11243367:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -24841,143 +24993,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 11243501 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb73", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "value": 11243367 } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-7811771c3f3344dca8b4fcf0f9fd84b1" - } - ], - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "criteria provided, single submitter" - } - } - ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328104" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410595.3" + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] + } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-7811771c3f3344dca8b4fcf0f9fd84b1", + ], + "id": "dv-3bd5a669b6b14313bb6585f4f0249b8e", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -24985,21 +25081,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -25008,18 +25092,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -25028,17 +25112,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -25047,99 +25131,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243591:G:T", - "display": "NC_000019.9:11243591:G:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.9:11243501:T:C", + "display": "NC_000019.9:11243501:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -25148,143 +25195,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 11243591 - } - } - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-62fab6a85932091e78c3bb75", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "value": 11243501 } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "diagnostic-implication" } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-a4bc1ce389c943248c967f087971ba88" - } - ], - "component": [ + }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "53037-8", - "display": "Genetic variation clinical significance" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA6675-8", - "display": "Benign" - } - ] + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "predicted phenotype" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.ncbi.nlm.nih.gov/medgen", - "code": "C0745103", - "display": "Hypercholesterolemia, familial, 1" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueCodeableConcept": { - "text": "criteria provided, single submitter" } } ], - "identifier": [ - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar", - "value": "328106" - }, - { - "system": "http://www.ncbi.nlm.nih.gov/clinvar/scv", - "value": "SCV000410597.3" - } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-a4bc1ce389c943248c967f087971ba88", + "id": "dv-5459aa2045a740c0af8c14cbc66cd4f2", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -25292,21 +25283,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -25315,18 +25294,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -25335,17 +25314,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -25354,18 +25333,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -25374,101 +25353,122 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "TCTA" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243734:C:T", - "display": "NC_000019.9:11243734:C:T" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243223:CTACTA:CTA", + "display": "NC_000019.9:11243223:CTACTA:CTA", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueRange": { + "low": { + "value": 11243222 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11243734 - } - } } - ] + ], + "id": "dv-d5e6a6a584a44454901740ac1d9c4b1f", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_haplotypes/1.json b/tests/expected_outputs/find_subject_haplotypes/1.json index b44edc51b..bc090eb49 100644 --- a/tests/expected_outputs/find_subject_haplotypes/1.json +++ b/tests/expected_outputs/find_subject_haplotypes/1.json @@ -1,5 +1,4 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "haplotypes", @@ -11,20 +10,12 @@ { "name": "genotype", "resource": { - "resourceType": "Observation", - "id": "dv-61ccfd4a072302a0eb2115c6", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -32,49 +23,58 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "84413-4", - "display": "Genotype display name" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.pharmvar.org", - "code": "CYP2D6 *1/*41", - "display": "CYP2D6 *1/*41" + "display": "Genotype display name", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "48018-6", - "display": "Gene studied" + "display": "Gene studied", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org/geneId", "code": "HGNC:2625", - "display": "CYP2D6" + "display": "CYP2D6", + "system": "http://www.genenames.org/geneId" } ] } } - ] + ], + "id": "dv-61ccfd4a072302a0eb2115c6", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "CYP2D6 *1/*41", + "display": "CYP2D6 *1/*41", + "system": "https://www.pharmvar.org" + } + ] + } } } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_haplotypes/2.json b/tests/expected_outputs/find_subject_haplotypes/2.json index 4c8f19fe7..f71ebbcfb 100644 --- a/tests/expected_outputs/find_subject_haplotypes/2.json +++ b/tests/expected_outputs/find_subject_haplotypes/2.json @@ -1,30 +1,21 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "haplotypes", "part": [ { "name": "geneItem", - "valueString": "HGNC:2625" + "valueString": "HGNC:2621" }, { "name": "genotype", "resource": { - "resourceType": "Observation", - "id": "dv-61ccfd4a072302a0eb2115c6", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -32,46 +23,54 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "84413-4", - "display": "Genotype display name" + "display": "Genotype display name", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.pharmvar.org", - "code": "CYP2D6 *1/*41", - "display": "CYP2D6 *1/*41" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK328" - }, "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "48018-6", - "display": "Gene studied" + "display": "Gene studied", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org/geneId", - "code": "HGNC:2625", - "display": "CYP2D6" + "code": "HGNC:2621", + "display": "CYP2C19", + "system": "http://www.genenames.org/geneId" } ] } } - ] + ], + "id": "dv-61ccfd4a072302a0eb2115c3", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "CYP2C19 *1/*17", + "display": "CYP2C19 *1/*17", + "system": "https://www.pharmvar.org" + } + ] + } } } ] @@ -81,25 +80,17 @@ "part": [ { "name": "geneItem", - "valueString": "HGNC:2621" + "valueString": "HGNC:2625" }, { "name": "genotype", "resource": { - "resourceType": "Observation", - "id": "dv-61ccfd4a072302a0eb2115c3", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -107,49 +98,58 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "84413-4", - "display": "Genotype display name" + "display": "Genotype display name", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.pharmvar.org", - "code": "CYP2C19 *1/*17", - "display": "CYP2C19 *1/*17" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK328" - }, "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "48018-6", - "display": "Gene studied" + "display": "Gene studied", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org/geneId", - "code": "HGNC:2621", - "display": "CYP2C19" + "code": "HGNC:2625", + "display": "CYP2D6", + "system": "http://www.genenames.org/geneId" } ] } } - ] + ], + "id": "dv-61ccfd4a072302a0eb2115c6", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "CYP2D6 *1/*41", + "display": "CYP2D6 *1/*41", + "system": "https://www.pharmvar.org" + } + ] + } } } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_haplotypes/3.json b/tests/expected_outputs/find_subject_haplotypes/3.json index da71db7f1..4509159ec 100644 --- a/tests/expected_outputs/find_subject_haplotypes/3.json +++ b/tests/expected_outputs/find_subject_haplotypes/3.json @@ -1,5 +1,4 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "haplotypes", @@ -11,20 +10,12 @@ { "name": "genotype", "resource": { - "resourceType": "Observation", - "id": "dv-61ccfd4a072302a0eb2115be", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -32,49 +23,58 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "84413-4", - "display": "Genotype display name" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://glstring.org", - "code": "hla#3.33.0#HLA-B*08:01/HLA-B*40:01", - "display": "hla#3.33.0#HLA-B*08:01/HLA-B*40:01" + "display": "Genotype display name", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "48018-6", - "display": "Gene studied" + "display": "Gene studied", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org/geneId", "code": "HGNC:4932", - "display": "HLA-B" + "display": "HLA-B", + "system": "http://www.genenames.org/geneId" } ] } } - ] + ], + "id": "dv-61ccfd4a072302a0eb2115be", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "hla#3.33.0#HLA-B*08:01/HLA-B*40:01", + "display": "hla#3.33.0#HLA-B*08:01/HLA-B*40:01", + "system": "http://glstring.org" + } + ] + } } } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_haplotypes/4.json b/tests/expected_outputs/find_subject_haplotypes/4.json index 1cc3bebb2..df2ae6231 100644 --- a/tests/expected_outputs/find_subject_haplotypes/4.json +++ b/tests/expected_outputs/find_subject_haplotypes/4.json @@ -1,5 +1,4 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "haplotypes", @@ -11,20 +10,12 @@ { "name": "genotype", "resource": { - "resourceType": "Observation", - "id": "dv-61ccfd4a072302a0eb2115be", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -32,49 +23,58 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "84413-4", - "display": "Genotype display name" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://glstring.org", - "code": "hla#3.33.0#HLA-B*08:01/HLA-B*40:01", - "display": "hla#3.33.0#HLA-B*08:01/HLA-B*40:01" + "display": "Genotype display name", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "48018-6", - "display": "Gene studied" + "display": "Gene studied", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org/geneId", "code": "HGNC:4932", - "display": "HLA-B" + "display": "HLA-B", + "system": "http://www.genenames.org/geneId" } ] } } - ] + ], + "id": "dv-61ccfd4a072302a0eb2115be", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "hla#3.33.0#HLA-B*08:01/HLA-B*40:01", + "display": "hla#3.33.0#HLA-B*08:01/HLA-B*40:01", + "system": "http://glstring.org" + } + ] + } } } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_molecular_consequences/1.json b/tests/expected_outputs/find_subject_molecular_consequences/1.json index 03311da48..40dff0846 100644 --- a/tests/expected_outputs/find_subject_molecular_consequences/1.json +++ b/tests/expected_outputs/find_subject_molecular_consequences/1.json @@ -1,27 +1,18 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "consequence", "resource": { - "resourceType": "Observation", - "id": "dv-665f9fd66ee6113688ebd5b4", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "GE", + "system": "http://terminology.hl7.org/CodeSystem/v2-0074" }, { - "system": "http://terminology.hl7.org/CodeSystem/v2-0074", - "code": "GE" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -29,27 +20,19 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "molecular-consequences" + "code": "molecular-consequences", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/TCGA-DD-A1EH" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-86ab0ee2a6d940c08534ed2db6019d69" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "48004-6", - "display": "DNA change (c.HGVS)" + "display": "DNA change (c.HGVS)", + "system": "http://loinc.org" } ] }, @@ -61,75 +44,83 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51958-7", - "display": "Reference Transcript" + "code": "48005-3", + "display": "Protein (Amino Acid) Change - pHGVS", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "NM_178349.2" + "text": "p.Val40Phe" } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48005-3", - "display": "Protein (Amino Acid) Change - pHGVS" + "code": "51958-7", + "display": "Reference Transcript", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "p.Val40Phe" + "text": "NM_178349.2" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "feature-consequence", - "display": "Feature Consequence" + "display": "Feature Consequence", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://sequenceontology.org", "code": "SO:0001583", - "display": "missense_variant" + "display": "missense_variant", + "system": "http://sequenceontology.org" } ] } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-86ab0ee2a6d940c08534ed2db6019d69" + } + ], + "id": "dv-665f9fd66ee6113688ebd5b4", "interpretation": [ { "text": "MODERATE" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-86ab0ee2a6d940c08534ed2db6019d69", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/TCGA-DD-A1EH" + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -137,21 +128,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/TCGA-DD-A1EH" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -160,18 +139,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6684-0", - "display": "somatic" + "display": "somatic", + "system": "http://loinc.org" } ] } @@ -180,17 +159,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000001.10" + "code": "NC_000001.10", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -199,101 +178,122 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "G" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000001.10:152785039:G:T", - "display": "NC_000001.10:152785039:G:T" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000001.10:152785039:G:T", + "display": "NC_000001.10:152785039:G:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueRange": { + "low": { + "value": 152785039 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 152785039 - } - } } - ] + ], + "id": "dv-86ab0ee2a6d940c08534ed2db6019d69", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/TCGA-DD-A1EH" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_molecular_consequences/2.json b/tests/expected_outputs/find_subject_molecular_consequences/2.json index b31c93d61..2d4f63c0d 100644 --- a/tests/expected_outputs/find_subject_molecular_consequences/2.json +++ b/tests/expected_outputs/find_subject_molecular_consequences/2.json @@ -1,27 +1,18 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "consequence", "resource": { - "resourceType": "Observation", - "id": "dv-666319b7b66532ba5a99b4a3", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "GE", + "system": "http://terminology.hl7.org/CodeSystem/v2-0074" }, { - "system": "http://terminology.hl7.org/CodeSystem/v2-0074", - "code": "GE" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -29,27 +20,19 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "molecular-consequences" + "code": "molecular-consequences", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NA19240" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-92ee36e45955474c9a8fe16b69086e83" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "48004-6", - "display": "DNA change (c.HGVS)" + "display": "DNA change (c.HGVS)", + "system": "http://loinc.org" } ] }, @@ -61,9 +44,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51958-7", - "display": "Reference Transcript" + "code": "48005-3", + "display": "Protein (Amino Acid) Change - pHGVS", + "system": "http://loinc.org" } ] }, @@ -75,9 +58,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48005-3", - "display": "Protein (Amino Acid) Change - pHGVS" + "code": "51958-7", + "display": "Reference Transcript", + "system": "http://loinc.org" } ] }, @@ -89,18 +72,18 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "feature-consequence", - "display": "Feature Consequence" + "display": "Feature Consequence", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://sequenceontology.org", "code": "SO:0001589", - "display": "frameshift_variant" + "display": "frameshift_variant", + "system": "http://sequenceontology.org" } ] } @@ -109,47 +92,55 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "functional-effect", - "display": "Functional Effect" + "display": "Functional Effect", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://sequenceontology.org", "code": "SO:0002054", - "display": "loss_of_function_variant" + "display": "loss_of_function_variant", + "system": "http://sequenceontology.org" } ] } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-92ee36e45955474c9a8fe16b69086e83" + } + ], + "id": "dv-666319b7b66532ba5a99b4a3", "interpretation": [ { "text": "HIGH" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-92ee36e45955474c9a8fe16b69086e83", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NA19240" + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -157,21 +148,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NA19240" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -180,18 +159,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -200,17 +179,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000003.11" + "code": "NC_000003.11", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -219,18 +198,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -239,29 +218,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000003.11:37050303:G:A", - "display": "NC_000003.11:37050303:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -271,9 +230,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, @@ -283,18 +242,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000003.11:37050303:G:A", + "display": "NC_000003.11:37050303:G:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -303,9 +262,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, @@ -314,9 +273,50 @@ "value": 37050303 } } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] + } } - ] + ], + "id": "dv-92ee36e45955474c9a8fe16b69086e83", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NA19240" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_molecular_consequences/3.json b/tests/expected_outputs/find_subject_molecular_consequences/3.json index 71b64d6a2..1dabce72a 100644 --- a/tests/expected_outputs/find_subject_molecular_consequences/3.json +++ b/tests/expected_outputs/find_subject_molecular_consequences/3.json @@ -1,3 +1,3 @@ { - "resourceType": "Parameters" + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_specific_haplotypes/1.json b/tests/expected_outputs/find_subject_specific_haplotypes/1.json index bc89f322a..ecf188e45 100644 --- a/tests/expected_outputs/find_subject_specific_haplotypes/1.json +++ b/tests/expected_outputs/find_subject_specific_haplotypes/1.json @@ -1,34 +1,17 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "haplotypes", "part": [ - { - "name": "haplotypeItem", - "valueString": "CYP2C19" - }, - { - "name": "presence", - "valueBoolean": true - }, { "name": "genotype", "resource": { - "resourceType": "Observation", - "id": "dv-61ccfd4a072302a0eb2115ca", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -36,49 +19,66 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "84413-4", - "display": "Genotype display name" + "display": "Genotype display name", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.pharmvar.org", - "code": "CYP2C19 *1/*1", - "display": "CYP2C19 *1/*1" - } - ] - }, - "subject": { - "reference": "Patient/XYZ123" - }, "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "48018-6", - "display": "Gene studied" + "display": "Gene studied", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org/geneId", "code": "HGNC:2621", - "display": "CYP2C19" + "display": "CYP2C19", + "system": "http://www.genenames.org/geneId" } ] } } - ] + ], + "id": "dv-61ccfd4a072302a0eb2115ca", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/XYZ123" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "CYP2C19 *1/*1", + "display": "CYP2C19 *1/*1", + "system": "https://www.pharmvar.org" + } + ] + } } + }, + { + "name": "haplotypeItem", + "valueString": "CYP2C19" + }, + { + "name": "presence", + "valueBoolean": true } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_specific_haplotypes/2.json b/tests/expected_outputs/find_subject_specific_haplotypes/2.json index bbf73a467..10d4d9e41 100644 --- a/tests/expected_outputs/find_subject_specific_haplotypes/2.json +++ b/tests/expected_outputs/find_subject_specific_haplotypes/2.json @@ -1,5 +1,4 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "haplotypes", @@ -14,5 +13,6 @@ } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_specific_haplotypes/3.json b/tests/expected_outputs/find_subject_specific_haplotypes/3.json index 1099ee8b5..53a909e79 100644 --- a/tests/expected_outputs/find_subject_specific_haplotypes/3.json +++ b/tests/expected_outputs/find_subject_specific_haplotypes/3.json @@ -1,84 +1,84 @@ { - "resourceType": "Parameters", - "parameter": [ - { - "name": "haplotypes", - "part": [ + "parameter": [ { - "name": "haplotypeItem", - "valueString": "DRB1*13:02" - }, - { - "name": "presence", - "valueBoolean": true - }, - { - "name": "genotype", - "resource": { - "resourceType": "Observation", - "id": "dv-675b7f8e910c42bf52d8828b", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ + "name": "haplotypes", + "part": [ { - "system": "http://loinc.org", - "code": "84413-4", - "display": "Genotype display name" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ebi.ac.uk/ipd/imgt/hla", - "code": "DRB1*13:AKBAR", - "display": "DRB1*13:AKBAR" - } - ] - }, - "subject": { - "reference": "Patient/XYZ234" - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48018-6", - "display": "Gene studied" + "name": "genotype", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "84413-4", + "display": "Genotype display name", + "system": "http://loinc.org" + } + ] + }, + "component": [ + { + "code": { + "coding": [ + { + "code": "48018-6", + "display": "Gene studied", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "HGNC:4948", + "display": "HLA-DRB1", + "system": "http://www.genenames.org/geneId" + } + ] + } + } + ], + "id": "dv-675b7f8e910c42bf52d8828b", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/XYZ234" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "DRB1*13:AKBAR", + "display": "DRB1*13:AKBAR", + "system": "http://www.ebi.ac.uk/ipd/imgt/hla" + } + ] + } } - ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.genenames.org/geneId", - "code": "HGNC:4948", - "display": "HLA-DRB1" - } - ] + { + "name": "haplotypeItem", + "valueString": "DRB1*13:02" + }, + { + "name": "presence", + "valueBoolean": true } - } ] - } } - ] - } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_specific_variants/1.json b/tests/expected_outputs/find_subject_specific_variants/1.json index 037e8486f..ce5a24b0b 100644 --- a/tests/expected_outputs/find_subject_specific_variants/1.json +++ b/tests/expected_outputs/find_subject_specific_variants/1.json @@ -1,13 +1,8 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ - { - "name": "variantItem", - "valueString": "NC_000005.9:g.112102032A>T" - }, { "name": "presence", "valueBoolean": true @@ -15,20 +10,12 @@ { "name": "variant", "resource": { - "resourceType": "Observation", - "id": "dv-8946090cf8ec4bd78f0ca4a8ee32b3c7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -36,21 +23,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/m123" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -59,37 +34,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000005.9" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000005.9:112102031:A:T", - "display": "NC_000005.9:112102031:A:T" + "code": "NC_000005.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -98,9 +53,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -110,9 +65,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, @@ -122,18 +77,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000005.9:112102031:A:T", + "display": "NC_000005.9:112102031:A:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -142,9 +97,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, @@ -153,11 +108,56 @@ "value": 112102031 } } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] + } } - ] + ], + "id": "dv-8946090cf8ec4bd78f0ca4a8ee32b3c7", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/m123" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } + }, + { + "name": "variantItem", + "valueString": "NC_000005.9:g.112102032A>T" } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_specific_variants/2.json b/tests/expected_outputs/find_subject_specific_variants/2.json index 443fb911a..215ac3ee0 100644 --- a/tests/expected_outputs/find_subject_specific_variants/2.json +++ b/tests/expected_outputs/find_subject_specific_variants/2.json @@ -1,13 +1,8 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ - { - "name": "variantItem", - "valueString": "NM_001127510.3:c.145A>T" - }, { "name": "presence", "valueBoolean": true @@ -15,20 +10,12 @@ { "name": "variant", "resource": { - "resourceType": "Observation", - "id": "dv-8946090cf8ec4bd78f0ca4a8ee32b3c7", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -36,21 +23,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/m123" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -59,37 +34,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000005.9" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000005.9:112102031:A:T", - "display": "NC_000005.9:112102031:A:T" + "code": "NC_000005.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -98,9 +53,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -110,9 +65,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, @@ -122,18 +77,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000005.9:112102031:A:T", + "display": "NC_000005.9:112102031:A:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -142,9 +97,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, @@ -153,11 +108,56 @@ "value": 112102031 } } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] + } } - ] + ], + "id": "dv-8946090cf8ec4bd78f0ca4a8ee32b3c7", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/m123" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } + }, + { + "name": "variantItem", + "valueString": "NM_001127510.3:c.145A>T" } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_specific_variants/3.json b/tests/expected_outputs/find_subject_specific_variants/3.json index 79b089712..5814f428a 100644 --- a/tests/expected_outputs/find_subject_specific_variants/3.json +++ b/tests/expected_outputs/find_subject_specific_variants/3.json @@ -1,96 +1,96 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ - { - "name": "variantItem", - "valueString": "NC_000005.9:112154946:CC:C" - }, { "name": "presence", "valueBoolean": false + }, + { + "name": "variantItem", + "valueString": "NC_000005.9:112154946:CC:C" } ] }, { "name": "variants", "part": [ - { - "name": "variantItem", - "valueString": "NC_000005.9:112157612:C:T" - }, { "name": "presence", "valueBoolean": false + }, + { + "name": "variantItem", + "valueString": "NC_000005.9:112157612:C:T" } ] }, { "name": "variants", "part": [ - { - "name": "variantItem", - "valueString": "NC_000017.10:41246373:G:" - }, { "name": "presence", "valueBoolean": false + }, + { + "name": "variantItem", + "valueString": "NC_000013.10:32900284:C:A" } ] }, { "name": "variants", "part": [ - { - "name": "variantItem", - "valueString": "NC_000017.10:41243854:AAA:AAAA" - }, { "name": "presence", "valueBoolean": false + }, + { + "name": "variantItem", + "valueString": "NC_000014.8:23894101:A:T" } ] }, { "name": "variants", "part": [ - { - "name": "variantItem", - "valueString": "NC_000013.10:32900284:C:A" - }, { "name": "presence", "valueBoolean": false + }, + { + "name": "variantItem", + "valueString": "NC_000017.10:41243854:AAA:AAAA" } ] }, { "name": "variants", "part": [ - { - "name": "variantItem", - "valueString": "NC_000019.9:11216262:C:A" - }, { "name": "presence", "valueBoolean": false + }, + { + "name": "variantItem", + "valueString": "NC_000017.10:41246373:G:" } ] }, { "name": "variants", "part": [ - { - "name": "variantItem", - "valueString": "NC_000014.8:23894101:A:T" - }, { "name": "presence", "valueBoolean": false + }, + { + "name": "variantItem", + "valueString": "NC_000019.9:11216262:C:A" } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_structural_intersecting_variants/1.json b/tests/expected_outputs/find_subject_structural_intersecting_variants/1.json index 019fe688e..ae32b8067 100644 --- a/tests/expected_outputs/find_subject_structural_intersecting_variants/1.json +++ b/tests/expected_outputs/find_subject_structural_intersecting_variants/1.json @@ -1,31 +1,31 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ - { - "name": "rangeItem", - "valueString": "NC_000007.14:55019016-55211628" - }, { "name": "presence", "valueBoolean": false + }, + { + "name": "rangeItem", + "valueString": "NC_000004.12:54727415-54727542" } ] }, { "name": "variants", "part": [ - { - "name": "rangeItem", - "valueString": "NC_000004.12:54727415-54727542" - }, { "name": "presence", "valueBoolean": false + }, + { + "name": "rangeItem", + "valueString": "NC_000007.14:55019016-55211628" } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_structural_intersecting_variants/2.json b/tests/expected_outputs/find_subject_structural_intersecting_variants/2.json index dfe9ba73f..8614b24c8 100644 --- a/tests/expected_outputs/find_subject_structural_intersecting_variants/2.json +++ b/tests/expected_outputs/find_subject_structural_intersecting_variants/2.json @@ -1,34 +1,25 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ - { - "name": "rangeItem", - "valueString": "NC_000002.12:179400709-179483218" - }, { "name": "presence", "valueBoolean": true }, + { + "name": "rangeItem", + "valueString": "NC_000002.12:179400709-179483218" + }, { "name": "variant", "resource": { - "resourceType": "Observation", - "id": "dv-da1622b8a3e84c6caba59a6b5dd0cf34", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -36,21 +27,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/ABC789" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -59,18 +38,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48019-4", - "display": "DNA Change Type" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://sequenceontology.org", - "code": "SO:0000159", - "display": "deletion" + "code": "NC_000002.11", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -79,17 +57,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "48019-4", + "display": "DNA Change Type", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000002.11" + "code": "SO:0000159", + "display": "deletion", + "system": "http://sequenceontology.org" } ] } @@ -98,92 +77,113 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "82155-3", - "display": "Genomic Structural Variant copy Number" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81301-4", + "display": "Variant outer start-end", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueRange": { + "high": { + "value": 179483050 + }, + "low": { + "value": 179401194 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81302-2", + "display": "Variant inner start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "valueRange": { + "high": { + "value": 179482950 + }, + "low": { + "value": 179401294 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81301-4", - "display": "Variant outer start-end" + "code": "82155-3", + "display": "Genomic Structural Variant copy Number", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 179401194 - }, - "high": { - "value": 179483050 - } + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 1 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81302-2", - "display": "Variant inner start-end" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 179401294 - }, - "high": { - "value": 179482950 - } + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] + ], + "id": "dv-da1622b8a3e84c6caba59a6b5dd0cf34", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/ABC789" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_structural_intersecting_variants/3.json b/tests/expected_outputs/find_subject_structural_intersecting_variants/3.json index a836bb76c..3fa321b2e 100644 --- a/tests/expected_outputs/find_subject_structural_intersecting_variants/3.json +++ b/tests/expected_outputs/find_subject_structural_intersecting_variants/3.json @@ -1,47 +1,38 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ - { - "name": "rangeItem", - "valueString": "NC_000017.11:43044294-43125364" - }, { "name": "presence", "valueBoolean": false + }, + { + "name": "rangeItem", + "valueString": "NC_000017.11:43044294-43125364" } ] }, { "name": "variants", "part": [ - { - "name": "rangeItem", - "valueString": "NC_000013.11:32315507-32400268" - }, { "name": "presence", "valueBoolean": true }, + { + "name": "rangeItem", + "valueString": "NC_000013.11:32315507-32400268" + }, { "name": "variant", "resource": { - "resourceType": "Observation", - "id": "dv-d77a942f939d49659f1e87a83d7eb255", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -49,21 +40,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HCC1143" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -72,18 +51,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48019-4", - "display": "DNA Change Type" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://sequenceontology.org", - "code": "SO:0000159", - "display": "deletion" + "code": "LA6684-0", + "display": "somatic", + "system": "http://loinc.org" } ] } @@ -92,18 +71,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6684-0", - "display": "somatic" + "code": "NC_000013.10", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -112,17 +90,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "48019-4", + "display": "DNA Change Type", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000013.10" + "code": "SO:0000159", + "display": "deletion", + "system": "http://sequenceontology.org" } ] } @@ -131,9 +110,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -143,38 +122,37 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81301-4", + "display": "Variant outer start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "valueRange": { + "high": { + "value": 49362068 + }, + "low": { + "value": 24055052 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81301-4", - "display": "Variant outer start-end" + "code": "81302-2", + "display": "Variant inner start-end", + "system": "http://loinc.org" } ] }, "valueRange": { - "low": { - "value": 24055052 - }, "high": { - "value": 49362068 + "value": 49362048 + }, + "low": { + "value": 24055072 } } }, @@ -182,25 +160,47 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81302-2", - "display": "Variant inner start-end" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 24055072 - }, - "high": { - "value": 49362048 - } + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] + ], + "id": "dv-d77a942f939d49659f1e87a83d7eb255", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/HCC1143" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_structural_subsuming_variants/1.json b/tests/expected_outputs/find_subject_structural_subsuming_variants/1.json index a208eba52..48b21326d 100644 --- a/tests/expected_outputs/find_subject_structural_subsuming_variants/1.json +++ b/tests/expected_outputs/find_subject_structural_subsuming_variants/1.json @@ -1,34 +1,25 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ - { - "name": "rangeItem", - "valueString": "NC_000007.14:116672195-116798386" - }, { "name": "presence", "valueBoolean": true }, + { + "name": "rangeItem", + "valueString": "NC_000007.14:116672195-116798386" + }, { "name": "variant", "resource": { - "resourceType": "Observation", - "id": "dv-87ca3273153f4202a878863a1d96f213", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -36,21 +27,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HCC1143" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -59,18 +38,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48019-4", - "display": "DNA Change Type" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://sequenceontology.org", - "code": "SO:1000035", - "display": "duplication" + "code": "LA6684-0", + "display": "somatic", + "system": "http://loinc.org" } ] } @@ -79,18 +58,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6684-0", - "display": "somatic" + "code": "NC_000007.13", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -99,17 +77,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "48019-4", + "display": "DNA Change Type", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.13" + "code": "SO:1000035", + "display": "duplication", + "system": "http://sequenceontology.org" } ] } @@ -118,9 +97,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -130,38 +109,37 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81301-4", + "display": "Variant outer start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "valueRange": { + "high": { + "value": 129038244 + }, + "low": { + "value": 66028223 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81301-4", - "display": "Variant outer start-end" + "code": "81302-2", + "display": "Variant inner start-end", + "system": "http://loinc.org" } ] }, "valueRange": { - "low": { - "value": 66028223 - }, "high": { - "value": 129038244 + "value": 129038224 + }, + "low": { + "value": 66028243 } } }, @@ -169,25 +147,47 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81302-2", - "display": "Variant inner start-end" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 66028243 - }, - "high": { - "value": 129038224 - } + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] + ], + "id": "dv-87ca3273153f4202a878863a1d96f213", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/HCC1143" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_structural_subsuming_variants/2.json b/tests/expected_outputs/find_subject_structural_subsuming_variants/2.json index a208eba52..48b21326d 100644 --- a/tests/expected_outputs/find_subject_structural_subsuming_variants/2.json +++ b/tests/expected_outputs/find_subject_structural_subsuming_variants/2.json @@ -1,34 +1,25 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ - { - "name": "rangeItem", - "valueString": "NC_000007.14:116672195-116798386" - }, { "name": "presence", "valueBoolean": true }, + { + "name": "rangeItem", + "valueString": "NC_000007.14:116672195-116798386" + }, { "name": "variant", "resource": { - "resourceType": "Observation", - "id": "dv-87ca3273153f4202a878863a1d96f213", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -36,21 +27,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HCC1143" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -59,18 +38,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48019-4", - "display": "DNA Change Type" + "code": "48002-0", + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://sequenceontology.org", - "code": "SO:1000035", - "display": "duplication" + "code": "LA6684-0", + "display": "somatic", + "system": "http://loinc.org" } ] } @@ -79,18 +58,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48002-0", - "display": "Genomic Source Class" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6684-0", - "display": "somatic" + "code": "NC_000007.13", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -99,17 +77,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "48019-4", + "display": "DNA Change Type", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.13" + "code": "SO:1000035", + "display": "duplication", + "system": "http://sequenceontology.org" } ] } @@ -118,9 +97,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -130,38 +109,37 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81301-4", + "display": "Variant outer start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "valueRange": { + "high": { + "value": 129038244 + }, + "low": { + "value": 66028223 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81301-4", - "display": "Variant outer start-end" + "code": "81302-2", + "display": "Variant inner start-end", + "system": "http://loinc.org" } ] }, "valueRange": { - "low": { - "value": 66028223 - }, "high": { - "value": 129038244 + "value": 129038224 + }, + "low": { + "value": 66028243 } } }, @@ -169,25 +147,47 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81302-2", - "display": "Variant inner start-end" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 66028243 - }, - "high": { - "value": 129038224 - } + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] + ], + "id": "dv-87ca3273153f4202a878863a1d96f213", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/HCC1143" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_structural_subsuming_variants/3.json b/tests/expected_outputs/find_subject_structural_subsuming_variants/3.json index 0ff20be2e..f22349b7d 100644 --- a/tests/expected_outputs/find_subject_structural_subsuming_variants/3.json +++ b/tests/expected_outputs/find_subject_structural_subsuming_variants/3.json @@ -1,34 +1,25 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ - { - "name": "rangeItem", - "valueString": "NC_000022.10:42522500-42526812" - }, { "name": "presence", "valueBoolean": true }, + { + "name": "rangeItem", + "valueString": "NC_000022.10:42522500-42526812" + }, { "name": "variant", "resource": { - "resourceType": "Observation", - "id": "dv-5daa556853884f0cad0ef1333d17b50d", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -36,21 +27,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/ABC789" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -59,18 +38,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48019-4", - "display": "DNA Change Type" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://sequenceontology.org", - "code": "SO:0000159", - "display": "deletion" + "code": "NC_000022.10", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -79,17 +57,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "48019-4", + "display": "DNA Change Type", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000022.10" + "code": "SO:0000159", + "display": "deletion", + "system": "http://sequenceontology.org" } ] } @@ -98,92 +77,113 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "82155-3", - "display": "Genomic Structural Variant copy Number" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "valueString": "N" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81301-4", + "display": "Variant outer start-end", + "system": "http://loinc.org" } ] }, - "valueString": "N" + "valueRange": { + "high": { + "value": 42528050 + }, + "low": { + "value": 42520950 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81302-2", + "display": "Variant inner start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "valueRange": { + "high": { + "value": 42527950 + }, + "low": { + "value": 42521050 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81301-4", - "display": "Variant outer start-end" + "code": "82155-3", + "display": "Genomic Structural Variant copy Number", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 42520950 - }, - "high": { - "value": 42528050 - } + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 1 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81302-2", - "display": "Variant inner start-end" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 42521050 - }, - "high": { - "value": 42527950 - } + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] + ], + "id": "dv-5daa556853884f0cad0ef1333d17b50d", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/ABC789" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_tx_implications/1.json b/tests/expected_outputs/find_subject_tx_implications/1.json index 97e7cd3f5..3e94a219b 100644 --- a/tests/expected_outputs/find_subject_tx_implications/1.json +++ b/tests/expected_outputs/find_subject_tx_implications/1.json @@ -1,23 +1,14 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "implication", "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae561", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -25,36 +16,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:3908", - "display": "Lung Non-small Cell Carcinoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -63,80 +46,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:3908", + "display": "Lung Non-small Cell Carcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Resistance" + "text": "Supports Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae580", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "5958" }, { - "system": "https://civicdb.org/evidence", - "value": "91" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -144,21 +135,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -167,17 +145,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "code": "1424911", + "display": "Dabrafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -186,18 +165,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" + "code": "1425099", + "display": "Trametinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -206,98 +185,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "DOID:3908", + "display": "Lung Non-small Cell Carcinoma", + "system": "https://disease-ontology.org" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "A (Validated association)" } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae8f5", + "identifier": [ + { + "system": "https://civicdb.org/evidence", + "value": "3017" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae580", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -305,36 +274,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:3908", - "display": "Lung Non-small Cell Carcinoma" + "code": "1424911", + "display": "Dabrafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -343,80 +304,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:3908", + "display": "Lung Non-small Cell Carcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Supports Resistance" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae561", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "91" }, { - "system": "https://civicdb.org/evidence", - "value": "5958" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae8f5", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -424,36 +393,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:3908", - "display": "Lung Non-small Cell Carcinoma" + "code": "NC_000007.14", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -462,32 +423,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "text": "A (Validated association)" - } + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "T" + }, + { + "code": { + "coding": [ + { + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" + "code": "NC_000007.14:140753335:A:T", + "display": "NC_000007.14:140753335:A:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -496,48 +467,77 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 140753335 + } + } + }, + { + "code": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 3.97994e-06 } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "3017" - } - ] + "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/CA12345" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_tx_implications/2.json b/tests/expected_outputs/find_subject_tx_implications/2.json index d7fdd0e16..5e5d88498 100644 --- a/tests/expected_outputs/find_subject_tx_implications/2.json +++ b/tests/expected_outputs/find_subject_tx_implications/2.json @@ -1,23 +1,14 @@ { - "resourceType": "Parameters", "parameter": [ { - "name": "implication", + "name": "genotype", "resource": { - "resourceType": "Observation", - "id": "dv-631a4ae712d58a72041f91ac", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -25,94 +16,65 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "84413-4", + "display": "Genotype display name", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-61ccfd4a072302a0eb2115c6" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "CPIC Level A" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "48018-6", + "display": "Gene studied", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "704", - "display": "Amitriptyline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "code": "HGNC:2621", + "display": "CYP2C19", + "system": "http://www.genenames.org/geneId" } ] - }, - "valueCodeableConcept": { - "text": "Normal Metabolizer" } } ], - "identifier": [ - { - "system": "https://www.pharmgkb.org", - "value": "PA128" - } - ] - } - }, - { - "name": "genotype", - "resource": { - "resourceType": "Observation", - "id": "dv-61ccfd4a072302a0eb2115c6", + "id": "dv-61ccfd4a072302a0eb2115c3", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "CYP2C19 *1/*17", + "display": "CYP2C19 *1/*17", + "system": "https://www.pharmvar.org" + } + ] + } + } + }, + { + "name": "genotype", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -120,65 +82,65 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "84413-4", - "display": "Genotype display name" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.pharmvar.org", - "code": "CYP2D6 *1/*41", - "display": "CYP2D6 *1/*41" + "display": "Genotype display name", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "48018-6", - "display": "Gene studied" + "display": "Gene studied", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org/geneId", "code": "HGNC:2625", - "display": "CYP2D6" + "display": "CYP2D6", + "system": "http://www.genenames.org/geneId" } ] } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-631a4ae012d58a72041f3aba", + ], + "id": "dv-61ccfd4a072302a0eb2115c6", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "CYP2D6 *1/*41", + "display": "CYP2D6 *1/*41", + "system": "https://www.pharmvar.org" + } + ] + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -186,61 +148,53 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-61ccfd4a072302a0eb2115c3" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "CPIC Level A" + "coding": [ + { + "code": "704", + "display": "Amitriptyline", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "704", - "display": "Amitriptyline" - } - ] + "text": "CPIC Level A" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -249,31 +203,39 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-61ccfd4a072302a0eb2115c3" + } + ], + "id": "dv-631a4ae012d58a72041f3aba", "identifier": [ { "system": "https://www.pharmgkb.org", "value": "PA124" } - ] - } - }, - { - "name": "genotype", - "resource": { - "resourceType": "Observation", - "id": "dv-61ccfd4a072302a0eb2115c3", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -281,47 +243,85 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "84413-4", - "display": "Genotype display name" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.pharmvar.org", - "code": "CYP2C19 *1/*17", - "display": "CYP2C19 *1/*17" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48018-6", - "display": "Gene studied" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org/geneId", - "code": "HGNC:2621", - "display": "CYP2C19" + "code": "704", + "display": "Amitriptyline", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] + }, + "valueCodeableConcept": { + "text": "CPIC Level A" } + }, + { + "code": { + "coding": [ + { + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" + } + ] + }, + "valueCodeableConcept": { + "text": "Normal Metabolizer" + } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-61ccfd4a072302a0eb2115c6" } - ] + ], + "id": "dv-631a4ae712d58a72041f91ac", + "identifier": [ + { + "system": "https://www.pharmgkb.org", + "value": "PA128" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + } } } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_tx_implications/3.json b/tests/expected_outputs/find_subject_tx_implications/3.json index 23334e24f..83342ff6e 100644 --- a/tests/expected_outputs/find_subject_tx_implications/3.json +++ b/tests/expected_outputs/find_subject_tx_implications/3.json @@ -1,23 +1,14 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "implication", "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae8dc", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -25,36 +16,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -63,43 +46,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "coding": [ + { + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -108,35 +91,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae569", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1398" }, { - "system": "https://civicdb.org/evidence", - "value": "1408" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -144,21 +135,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -167,17 +145,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -186,18 +165,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" } ] } @@ -206,98 +185,68 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "A" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" - } - ] - }, - "valueString": "T" - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae574", + "identifier": [ + { + "system": "https://civicdb.org/evidence", + "value": "1749" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae940", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -305,36 +254,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -343,43 +284,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "coding": [ + { + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -388,35 +329,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae57a", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "3750" }, { - "system": "https://civicdb.org/evidence", - "value": "8507" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae93e", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -424,36 +373,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -462,43 +403,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -507,35 +448,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae57b", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "3755" }, { - "system": "https://civicdb.org/evidence", - "value": "1421" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae917", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -543,36 +492,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -581,43 +522,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -626,35 +567,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae57c", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "3757" }, { - "system": "https://civicdb.org/evidence", - "value": "1902" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae582", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -662,36 +611,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -700,43 +641,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -745,35 +686,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae93e", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1421" }, { - "system": "https://civicdb.org/evidence", - "value": "5960" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae581", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -781,36 +730,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:2394", - "display": "Ovarian Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -819,80 +760,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "D (Preclinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Supports Resistance" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae560", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "90" }, { - "system": "https://civicdb.org/evidence", - "value": "5959" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae93f", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -900,36 +849,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:80522", - "display": "Thyroid Gland Anaplastic Carcinoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -938,43 +879,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:2394", + "display": "Ovarian Cancer", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -983,35 +924,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae581", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "5959" }, { - "system": "https://civicdb.org/evidence", - "value": "5961" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae56f", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1019,36 +968,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:285", - "display": "Hairy Cell Leukemia" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -1057,43 +998,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:285", + "display": "Hairy Cell Leukemia", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -1102,35 +1043,43 @@ } } ], - "identifier": [ + "derivedFrom": [ { - "system": "https://civicdb.org/variant", - "value": "12" - }, + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae56f", + "identifier": [ { "system": "https://civicdb.org/evidence", "value": "1579" + }, + { + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae57d", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1138,36 +1087,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:6812", - "display": "Childhood Pilocytic Astrocytoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -1176,43 +1117,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:2876", + "display": "Laryngeal Squamous Cell Carcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -1221,35 +1162,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae583", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "5962" }, { - "system": "https://civicdb.org/evidence", - "value": "3777" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae8f4", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1257,36 +1206,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:50626", - "display": "Gastrointestinal Neuroendocrine Tumor" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -1295,43 +1236,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:3908", + "display": "Lung Non-small Cell Carcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -1340,35 +1281,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae580", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "5958" }, { - "system": "https://civicdb.org/evidence", - "value": "1430" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae583", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1376,36 +1325,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:2876", - "display": "Laryngeal Squamous Cell Carcinoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -1414,43 +1355,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:3969", + "display": "Thyroid Gland Papillary Carcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -1459,35 +1400,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae570", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1591" }, { - "system": "https://civicdb.org/evidence", - "value": "5962" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae560", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1495,36 +1444,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -1533,80 +1474,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "coding": [ + { + "code": "DOID:3969", + "display": "Thyroid Gland Papillary Carcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Resistance" + "text": "Supports Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae58a", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "9018" }, { - "system": "https://civicdb.org/evidence", - "value": "90" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae56a", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1614,36 +1563,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -1652,80 +1593,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:3969", + "display": "Thyroid Gland Papillary Carcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Does Not Support Sensitivity/Response" + "text": "Supports Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae56e", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1414" }, { - "system": "https://civicdb.org/evidence", - "value": "1405" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae56e", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1733,36 +1682,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:3969", - "display": "Thyroid Gland Papillary Carcinoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -1771,43 +1712,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:4947", + "display": "Cholangiocarcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -1816,35 +1757,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae918", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "5906" }, { - "system": "https://civicdb.org/evidence", - "value": "1414" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae572", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1852,36 +1801,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9538", - "display": "Multiple Myeloma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -1890,43 +1831,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:50626", + "display": "Gastrointestinal Neuroendocrine Tumor", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -1935,35 +1876,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae8f4", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1430" }, { - "system": "https://civicdb.org/evidence", - "value": "1698" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae573", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1971,36 +1920,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9538", - "display": "Multiple Myeloma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -2009,43 +1950,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:50933", + "display": "Ovarian Serous Carcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2054,35 +1995,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae57e", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "3787" }, { - "system": "https://civicdb.org/evidence", - "value": "1699" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae589", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2090,36 +2039,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:7146", - "display": "Langerhans Cell Sarcoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -2128,43 +2069,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:6812", + "display": "Childhood Pilocytic Astrocytoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2173,35 +2114,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae57d", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "3777" }, { - "system": "https://civicdb.org/evidence", - "value": "7583" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae574", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2209,36 +2158,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -2247,43 +2188,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:7146", + "display": "Langerhans Cell Sarcoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2292,35 +2233,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae589", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "7583" }, { - "system": "https://civicdb.org/evidence", - "value": "1749" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae569", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2328,36 +2277,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -2366,43 +2307,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:80522", + "display": "Thyroid Gland Anaplastic Carcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2411,35 +2352,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae588", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "6045" }, { - "system": "https://civicdb.org/evidence", - "value": "1398" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae918", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2447,36 +2396,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:4947", - "display": "Cholangiocarcinoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -2485,43 +2426,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:80522", + "display": "Thyroid Gland Anaplastic Carcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2530,35 +2471,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae93f", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "5961" }, { - "system": "https://civicdb.org/evidence", - "value": "5906" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae562", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2566,36 +2515,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -2604,43 +2545,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "coding": [ + { + "code": "DOID:8923", + "display": "Skin Melanoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "A (Validated association)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2649,35 +2590,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae56c", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1409" }, { - "system": "https://civicdb.org/evidence", - "value": "99" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae8d5", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2685,36 +2634,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -2723,43 +2664,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "coding": [ + { + "code": "DOID:8923", + "display": "Skin Melanoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2768,35 +2709,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae56d", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1410" }, { - "system": "https://civicdb.org/evidence", - "value": "98" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae56d", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2804,36 +2753,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:8923", - "display": "Skin Melanoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -2842,80 +2783,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Does Not Support Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae56a", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1405" }, { - "system": "https://civicdb.org/evidence", - "value": "1410" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae570", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2923,36 +2872,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:3969", - "display": "Thyroid Gland Papillary Carcinoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -2961,80 +2902,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Does Not Support Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae93d", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1413" }, { - "system": "https://civicdb.org/evidence", - "value": "1591" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae580", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3042,36 +2991,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:3908", - "display": "Lung Non-small Cell Carcinoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -3080,43 +3021,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -3125,35 +3066,43 @@ } } ], - "identifier": [ + "derivedFrom": [ { - "system": "https://civicdb.org/variant", - "value": "12" - }, + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae917", + "identifier": [ { "system": "https://civicdb.org/evidence", - "value": "5958" + "value": "1902" + }, + { + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae56c", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3161,36 +3110,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:8923", - "display": "Skin Melanoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -3199,43 +3140,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "A (Validated association)" + "coding": [ + { + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -3244,35 +3185,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae582", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "5960" }, { - "system": "https://civicdb.org/evidence", - "value": "1409" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae588", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3280,36 +3229,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:80522", - "display": "Thyroid Gland Anaplastic Carcinoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -3318,43 +3259,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -3363,35 +3304,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae92a", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1589" }, { - "system": "https://civicdb.org/evidence", - "value": "6045" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae92a", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3399,36 +3348,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -3437,43 +3378,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "D (Preclinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -3482,35 +3423,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae562", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "99" }, { - "system": "https://civicdb.org/evidence", - "value": "1589" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae57e", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3518,36 +3467,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:50933", - "display": "Ovarian Serous Carcinoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -3556,43 +3497,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "D (Preclinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -3601,35 +3542,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae8d5", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "98" }, { - "system": "https://civicdb.org/evidence", - "value": "3787" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae919", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", - "category": [ + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3637,36 +3586,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -3675,43 +3616,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "coding": [ + { + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "D (Preclinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -3720,35 +3661,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae8dc", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1408" }, { - "system": "https://civicdb.org/evidence", - "value": "8506" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae93d", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3756,36 +3705,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -3794,80 +3735,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "D (Preclinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Does Not Support Sensitivity/Response" + "text": "Supports Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae919", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "8506" }, { - "system": "https://civicdb.org/evidence", - "value": "1413" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae57a", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3875,36 +3824,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -3913,43 +3854,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "D (Preclinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -3958,35 +3899,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae940", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "8507" }, { - "system": "https://civicdb.org/evidence", - "value": "3750" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae58a", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3994,36 +3943,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:3969", - "display": "Thyroid Gland Papillary Carcinoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -4032,43 +3973,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:9538", + "display": "Multiple Myeloma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -4077,35 +4018,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae572", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1698" }, { - "system": "https://civicdb.org/evidence", - "value": "9018" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae57c", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4113,36 +4062,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -4151,43 +4092,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:9538", + "display": "Multiple Myeloma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -4196,35 +4137,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae573", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1699" }, { - "system": "https://civicdb.org/evidence", - "value": "3757" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae57b", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4232,36 +4181,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "NC_000007.14", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -4270,32 +4211,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "T" + }, + { + "code": { + "coding": [ + { + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "NC_000007.14:140753335:A:T", + "display": "NC_000007.14:140753335:A:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -4304,28 +4255,77 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "valueRange": { + "low": { + "value": 140753335 + } } - } - ], - "identifier": [ + }, { - "system": "https://civicdb.org/variant", - "value": "12" + "code": { + "coding": [ + { + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" + } + ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 3.97994e-06 + } }, { - "system": "https://civicdb.org/evidence", - "value": "3755" + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] + } } - ] + ], + "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/CA12345" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_tx_implications/4.json b/tests/expected_outputs/find_subject_tx_implications/4.json index 305888562..f7d498f0c 100644 --- a/tests/expected_outputs/find_subject_tx_implications/4.json +++ b/tests/expected_outputs/find_subject_tx_implications/4.json @@ -1,23 +1,14 @@ { - "resourceType": "Parameters", "parameter": [ { - "name": "implication", + "name": "genotype", "resource": { - "resourceType": "Observation", - "id": "dv-631a4ae012d58a72041f3aba", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -25,94 +16,65 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "84413-4", + "display": "Genotype display name", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-61ccfd4a072302a0eb2115c3" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "CPIC Level A" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "48018-6", + "display": "Gene studied", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "704", - "display": "Amitriptyline" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "code": "HGNC:2621", + "display": "CYP2C19", + "system": "http://www.genenames.org/geneId" } ] - }, - "valueCodeableConcept": { - "text": "CYP2C19 Rapid Metabolizer" } } ], - "identifier": [ - { - "system": "https://www.pharmgkb.org", - "value": "PA124" - } - ] - } - }, - { - "name": "genotype", - "resource": { - "resourceType": "Observation", "id": "dv-61ccfd4a072302a0eb2115c3", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "CYP2C19 *1/*17", + "display": "CYP2C19 *1/*17", + "system": "https://www.pharmvar.org" + } + ] + } + } + }, + { + "name": "genotype", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -120,65 +82,65 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "84413-4", - "display": "Genotype display name" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.pharmvar.org", - "code": "CYP2C19 *1/*17", - "display": "CYP2C19 *1/*17" + "display": "Genotype display name", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "48018-6", - "display": "Gene studied" + "display": "Gene studied", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org/geneId", "code": "HGNC:2621", - "display": "CYP2C19" + "display": "CYP2C19", + "system": "http://www.genenames.org/geneId" } ] } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-631a4ae012d58a72041f3abb", + ], + "id": "dv-61ccfd4a072302a0eb2115c3", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "CYP2C19 *1/*17", + "display": "CYP2C19 *1/*17", + "system": "https://www.pharmvar.org" + } + ] + } + } + }, + { + "name": "genotype", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -186,94 +148,65 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "84413-4", + "display": "Genotype display name", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-61ccfd4a072302a0eb2115c3" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "CPIC Level A" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "48018-6", + "display": "Gene studied", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "32968", - "display": "clopidogrel" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "code": "HGNC:2621", + "display": "CYP2C19", + "system": "http://www.genenames.org/geneId" } ] - }, - "valueCodeableConcept": { - "text": "CYP2C19 Rapid Metabolizer" } } ], - "identifier": [ - { - "system": "https://www.pharmgkb.org", - "value": "PA124" - } - ] - } - }, - { - "name": "genotype", - "resource": { - "resourceType": "Observation", "id": "dv-61ccfd4a072302a0eb2115c3", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "CYP2C19 *1/*17", + "display": "CYP2C19 *1/*17", + "system": "https://www.pharmvar.org" + } + ] + } + } + }, + { + "name": "genotype", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -281,65 +214,65 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "84413-4", - "display": "Genotype display name" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.pharmvar.org", - "code": "CYP2C19 *1/*17", - "display": "CYP2C19 *1/*17" + "display": "Genotype display name", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "48018-6", - "display": "Gene studied" + "display": "Gene studied", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org/geneId", "code": "HGNC:2621", - "display": "CYP2C19" + "display": "CYP2C19", + "system": "http://www.genenames.org/geneId" } ] } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-631a4ae012d58a72041f3abc", + ], + "id": "dv-61ccfd4a072302a0eb2115c3", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "CYP2C19 *1/*17", + "display": "CYP2C19 *1/*17", + "system": "https://www.pharmvar.org" + } + ] + } + } + }, + { + "name": "genotype", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -347,94 +280,65 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "84413-4", + "display": "Genotype display name", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-61ccfd4a072302a0eb2115c3" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "CPIC Level A" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "48018-6", + "display": "Gene studied", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "2556", - "display": "Citalopram" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "code": "HGNC:2621", + "display": "CYP2C19", + "system": "http://www.genenames.org/geneId" } ] - }, - "valueCodeableConcept": { - "text": "CYP2C19 Rapid Metabolizer" } } ], - "identifier": [ - { - "system": "https://www.pharmgkb.org", - "value": "PA124" - } - ] - } - }, - { - "name": "genotype", - "resource": { - "resourceType": "Observation", "id": "dv-61ccfd4a072302a0eb2115c3", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "CYP2C19 *1/*17", + "display": "CYP2C19 *1/*17", + "system": "https://www.pharmvar.org" + } + ] + } + } + }, + { + "name": "genotype", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -442,65 +346,65 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "84413-4", - "display": "Genotype display name" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.pharmvar.org", - "code": "CYP2C19 *1/*17", - "display": "CYP2C19 *1/*17" + "display": "Genotype display name", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "48018-6", - "display": "Gene studied" + "display": "Gene studied", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org/geneId", - "code": "HGNC:2621", - "display": "CYP2C19" + "code": "HGNC:2625", + "display": "CYP2D6", + "system": "http://www.genenames.org/geneId" } ] } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-631a4ae012d58a72041f3ac2", + ], + "id": "dv-61ccfd4a072302a0eb2115c6", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "CYP2D6 *1/*41", + "display": "CYP2D6 *1/*41", + "system": "https://www.pharmvar.org" + } + ] + } + } + }, + { + "name": "genotype", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -508,94 +412,65 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "84413-4", + "display": "Genotype display name", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-61ccfd4a072302a0eb2115c3" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "CPIC Level A" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "48018-6", + "display": "Gene studied", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "321988", - "display": "Escitalopram" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "code": "HGNC:2625", + "display": "CYP2D6", + "system": "http://www.genenames.org/geneId" } ] - }, - "valueCodeableConcept": { - "text": "CYP2C19 Rapid Metabolizer" } } ], - "identifier": [ - { - "system": "https://www.pharmgkb.org", - "value": "PA124" - } - ] - } - }, - { - "name": "genotype", - "resource": { - "resourceType": "Observation", - "id": "dv-61ccfd4a072302a0eb2115c3", + "id": "dv-61ccfd4a072302a0eb2115c6", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "CYP2D6 *1/*41", + "display": "CYP2D6 *1/*41", + "system": "https://www.pharmvar.org" + } + ] + } + } + }, + { + "name": "genotype", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -603,65 +478,65 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "84413-4", - "display": "Genotype display name" + "display": "Genotype display name", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.pharmvar.org", - "code": "CYP2C19 *1/*17", - "display": "CYP2C19 *1/*17" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK328" - }, "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "48018-6", - "display": "Gene studied" + "display": "Gene studied", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org/geneId", - "code": "HGNC:2621", - "display": "CYP2C19" + "code": "HGNC:2625", + 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"http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1086,65 +940,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "84413-4", - "display": "Genotype display name" + "display": "Genotype display name", + "system": "http://loinc.org" } ] }, + "component": [ + { + "code": { + "coding": [ + { + "code": "48018-6", + "display": "Gene studied", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "HGNC:2625", + "display": "CYP2D6", + "system": "http://www.genenames.org/geneId" + } + ] + } + } + ], + "id": "dv-61ccfd4a072302a0eb2115c6", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + }, "valueCodeableConcept": { "coding": [ { - "system": "https://www.pharmvar.org", - "code": "CYP2D6 *1/*41", - "display": "CYP2D6 *1/*41" + "code": "CYP2D6 *1/*41", + "display": "CYP2D6 *1/*41", + "system": "https://www.pharmvar.org" + } + ] + } + } + }, + { + "name": "genotype", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "84413-4", + "display": "Genotype display name", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "48018-6", - "display": "Gene studied" + "display": "Gene studied", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org/geneId", "code": "HGNC:2625", - "display": "CYP2D6" + "display": "CYP2D6", + "system": "http://www.genenames.org/geneId" } ] } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-631a4ae712d58a72041f91a3", + ], + "id": "dv-61ccfd4a072302a0eb2115c6", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "CYP2D6 *1/*41", + "display": "CYP2D6 *1/*41", + "system": "https://www.pharmvar.org" + } + ] + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1152,61 +1072,53 @@ "code": { "coding": [ { - "system": 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"valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "26225", - "display": "Ondansetron" - } - ] + "text": "CPIC Level A" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -1215,31 +1127,39 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-61ccfd4a072302a0eb2115c6" + } + ], + "id": "dv-631a4ae712d58a72041f91a9", "identifier": [ { "system": "https://www.pharmgkb.org", "value": "PA128" } - ] - } - }, - { - "name": "genotype", - "resource": { - "resourceType": "Observation", - "id": "dv-61ccfd4a072302a0eb2115c6", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1247,65 +1167,94 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "84413-4", - "display": "Genotype display name" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.pharmvar.org", - "code": "CYP2D6 *1/*41", - "display": "CYP2D6 *1/*41" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, "component": [ { "code": { "coding": [ { - 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"id": "dv-631a4ae712d58a72041f91a5", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-61ccfd4a072302a0eb2115c6" + } + ], + "id": "dv-631a4ae712d58a72041f91ab", + "identifier": [ + { + "system": "https://www.pharmgkb.org", + "value": "PA128" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1313,94 +1262,94 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": 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"text": "CPIC Level A" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Normal Metabolizer" + "text": "CYP2C19 Rapid Metabolizer" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-61ccfd4a072302a0eb2115c3" + } + ], + "id": "dv-631a4ae012d58a72041f3ad0", "identifier": [ { "system": "https://www.pharmgkb.org", - "value": "PA128" + "value": "PA124" } - ] - } - }, - { - "name": "genotype", - "resource": { - "resourceType": "Observation", - "id": "dv-61ccfd4a072302a0eb2115c6", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" + 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"Observation", - "id": "dv-631a4ae712d58a72041f91a8", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-61ccfd4a072302a0eb2115c3" + } + ], + "id": "dv-631a4ae012d58a72041f3abc", + "identifier": [ + { + "system": "https://www.pharmgkb.org", + "value": "PA124" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1474,61 +1452,53 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": 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"text": "CPIC Level A" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -1537,31 +1507,39 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-61ccfd4a072302a0eb2115c6" + } + ], + "id": "dv-631a4ae712d58a72041f91a3", "identifier": [ { "system": "https://www.pharmgkb.org", "value": "PA128" } - ] - } - }, - { - "name": "genotype", - "resource": { - "resourceType": "Observation", - "id": "dv-61ccfd4a072302a0eb2115c6", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1569,65 +1547,94 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "84413-4", - "display": "Genotype display name" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.pharmvar.org", - "code": "CYP2D6 *1/*41", - "display": "CYP2D6 *1/*41" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48018-6", - "display": "Gene studied" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org/geneId", - "code": "HGNC:2625", - "display": "CYP2D6" + "code": "2670", + "display": "Codeine", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "text": "CPIC Level A" + } + }, + { + "code": { + "coding": [ + { + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] + }, + "valueCodeableConcept": { + "text": "Normal Metabolizer" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-631a4ae712d58a72041f91a9", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-61ccfd4a072302a0eb2115c6" + } + ], + "id": "dv-631a4ae712d58a72041f91a1", + "identifier": [ + { + "system": "https://www.pharmgkb.org", + "value": "PA128" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1635,61 +1642,53 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-61ccfd4a072302a0eb2115c6" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "CPIC Level A" + "coding": [ + { + "code": "27392", + "display": "tropisetron", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "10324", - "display": "Tamoxifen" - } - ] + "text": "CPIC Level A" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -1698,31 +1697,39 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-61ccfd4a072302a0eb2115c6" + } + ], + "id": "dv-631a4ae712d58a72041f91af", "identifier": [ { "system": "https://www.pharmgkb.org", "value": "PA128" } - ] - } - }, - { - "name": "genotype", - "resource": { - "resourceType": "Observation", - "id": "dv-61ccfd4a072302a0eb2115c6", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1730,65 +1737,94 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "84413-4", - "display": "Genotype display name" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.pharmvar.org", - "code": "CYP2D6 *1/*41", - "display": "CYP2D6 *1/*41" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48018-6", - "display": "Gene studied" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org/geneId", - "code": "HGNC:2625", - "display": "CYP2D6" + "code": "321988", + "display": "Escitalopram", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "text": "CPIC Level A" + } + }, + { + "code": { + "coding": [ + { + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] + }, + "valueCodeableConcept": { + "text": "CYP2C19 Rapid Metabolizer" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-631a4ae712d58a72041f91aa", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-61ccfd4a072302a0eb2115c3" + } + ], + "id": "dv-631a4ae012d58a72041f3ac2", + "identifier": [ + { + "system": "https://www.pharmgkb.org", + "value": "PA124" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1796,61 +1832,53 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-61ccfd4a072302a0eb2115c6" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "32937", + "display": "Paroxetine", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] - }, - "valueCodeableConcept": { - "text": "CPIC Level A" } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "38400", - "display": "atomoxetine" - } - ] + "text": "CPIC Level A" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -1859,31 +1887,39 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-61ccfd4a072302a0eb2115c6" + } + ], + "id": "dv-631a4ae712d58a72041f91a5", "identifier": [ { "system": "https://www.pharmgkb.org", "value": "PA128" } - ] - } - }, - { - "name": "genotype", - "resource": { - "resourceType": "Observation", - "id": "dv-61ccfd4a072302a0eb2115c6", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1891,65 +1927,94 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "84413-4", - "display": "Genotype display name" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.pharmvar.org", - "code": "CYP2D6 *1/*41", - "display": "CYP2D6 *1/*41" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48018-6", - "display": "Gene studied" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org/geneId", - "code": "HGNC:2625", - "display": "CYP2D6" + "code": "32968", + "display": "clopidogrel", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "text": "CPIC Level A" + } + }, + { + "code": { + "coding": [ + { + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] + }, + "valueCodeableConcept": { + "text": "CYP2C19 Rapid Metabolizer" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-631a4ae712d58a72041f91ab", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-61ccfd4a072302a0eb2115c3" + } + ], + "id": "dv-631a4ae012d58a72041f3abb", + "identifier": [ + { + "system": "https://www.pharmgkb.org", + "value": "PA124" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1957,61 +2022,53 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-61ccfd4a072302a0eb2115c6" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "CPIC Level A" + "coding": [ + { + "code": "38400", + "display": "atomoxetine", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "10689", - "display": "Tramadol" - } - ] + "text": "CPIC Level A" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2020,97 +2077,39 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-61ccfd4a072302a0eb2115c6" + } + ], + "id": "dv-631a4ae712d58a72041f91aa", "identifier": [ { "system": "https://www.pharmgkb.org", "value": "PA128" } - ] - } - }, - { - "name": "genotype", - "resource": { - "resourceType": "Observation", - "id": "dv-61ccfd4a072302a0eb2115c6", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "84413-4", - "display": "Genotype display name" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.pharmvar.org", - "code": "CYP2D6 *1/*41", - "display": "CYP2D6 *1/*41" - } - ] - }, "subject": { "reference": "Patient/NB6TK328" - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48018-6", - "display": "Gene studied" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.genenames.org/geneId", - "code": "HGNC:2625", - "display": "CYP2D6" - } - ] - } - } - ] + } } }, { "name": "implication", "resource": { - "resourceType": "Observation", - "id": "dv-631a4ae712d58a72041f91ac", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2118,61 +2117,53 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-61ccfd4a072302a0eb2115c6" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "CPIC Level A" + "coding": [ + { + "code": "42355", + "display": "Fluvoxamine", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "704", - "display": "Amitriptyline" - } - ] + "text": "CPIC Level A" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2181,97 +2172,39 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-61ccfd4a072302a0eb2115c6" + } + ], + "id": "dv-631a4ae712d58a72041f91a2", "identifier": [ { "system": "https://www.pharmgkb.org", "value": "PA128" } - ] - } - }, - { - "name": "genotype", - "resource": { - "resourceType": "Observation", - "id": "dv-61ccfd4a072302a0eb2115c6", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" - ] - }, - "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "84413-4", - "display": "Genotype display name" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.pharmvar.org", - "code": "CYP2D6 *1/*41", - "display": "CYP2D6 *1/*41" - } + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", + "status": "final", "subject": { "reference": "Patient/NB6TK328" - }, - "component": [ - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "48018-6", - "display": "Gene studied" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.genenames.org/geneId", - "code": "HGNC:2625", - "display": "CYP2D6" - } - ] - } - } - ] + } } }, { "name": "implication", "resource": { - "resourceType": "Observation", - "id": "dv-631a4ae712d58a72041f91ad", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2279,94 +2212,94 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-61ccfd4a072302a0eb2115c6" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "CPIC Level A" + "coding": [ + { + "code": "704", + "display": "Amitriptyline", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "7804", - "display": "Oxycodone" - } - ] + "text": "CPIC Level A" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Normal Metabolizer" + "text": "CYP2C19 Rapid Metabolizer" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-61ccfd4a072302a0eb2115c3" + } + ], + "id": "dv-631a4ae012d58a72041f3aba", "identifier": [ { "system": "https://www.pharmgkb.org", - "value": "PA128" + "value": "PA124" } - ] - } - }, - { - "name": "genotype", - "resource": { - "resourceType": "Observation", - "id": "dv-61ccfd4a072302a0eb2115c6", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2374,65 +2307,94 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "84413-4", - "display": "Genotype display name" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.pharmvar.org", - "code": "CYP2D6 *1/*41", - "display": "CYP2D6 *1/*41" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48018-6", - "display": "Gene studied" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org/geneId", - "code": "HGNC:2625", - "display": "CYP2D6" + "code": "704", + "display": "Amitriptyline", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "text": "CPIC Level A" + } + }, + { + "code": { + "coding": [ + { + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] + }, + "valueCodeableConcept": { + "text": "Normal Metabolizer" } } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-631a4ae712d58a72041f91af", + ], + "derivedFrom": [ + { + "reference": "Observation/dv-61ccfd4a072302a0eb2115c6" + } + ], + "id": "dv-631a4ae712d58a72041f91ac", + "identifier": [ + { + "system": "https://www.pharmgkb.org", + "value": "PA128" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2440,61 +2402,53 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-61ccfd4a072302a0eb2115c6" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "CPIC Level A" + "coding": [ + { + "code": "7531", + "display": "Nortriptyline", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "27392", - "display": "tropisetron" - } - ] + "text": "CPIC Level A" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2503,31 +2457,39 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-61ccfd4a072302a0eb2115c6" + } + ], + "id": "dv-631a4ae712d58a72041f91a8", "identifier": [ { "system": "https://www.pharmgkb.org", "value": "PA128" } - ] - } - }, - { - "name": "genotype", - "resource": { - "resourceType": "Observation", - "id": "dv-61ccfd4a072302a0eb2115c6", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2535,47 +2497,85 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "84413-4", - "display": "Genotype display name" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://www.pharmvar.org", - "code": "CYP2D6 *1/*41", - "display": "CYP2D6 *1/*41" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/NB6TK328" - }, "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48018-6", - "display": "Gene studied" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.genenames.org/geneId", - "code": "HGNC:2625", - "display": "CYP2D6" + "code": "7804", + "display": "Oxycodone", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "text": "CPIC Level A" + } + }, + { + "code": { + "coding": [ + { + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] + }, + "valueCodeableConcept": { + "text": "Normal Metabolizer" } } - ] + ], + "derivedFrom": [ + { + "reference": "Observation/dv-61ccfd4a072302a0eb2115c6" + } + ], + "id": "dv-631a4ae712d58a72041f91ad", + "identifier": [ + { + "system": "https://www.pharmgkb.org", + "value": "PA128" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/NB6TK328" + } } } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_tx_implications/5.json b/tests/expected_outputs/find_subject_tx_implications/5.json index 97e7cd3f5..3e94a219b 100644 --- a/tests/expected_outputs/find_subject_tx_implications/5.json +++ b/tests/expected_outputs/find_subject_tx_implications/5.json @@ -1,23 +1,14 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "implication", "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae561", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -25,36 +16,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:3908", - "display": "Lung Non-small Cell Carcinoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -63,80 +46,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:3908", + "display": "Lung Non-small Cell Carcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Resistance" + "text": "Supports Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae580", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "5958" }, { - "system": "https://civicdb.org/evidence", - "value": "91" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -144,21 +135,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -167,17 +145,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "code": "1424911", + "display": "Dabrafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -186,18 +165,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" + "code": "1425099", + "display": "Trametinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -206,98 +185,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "DOID:3908", + "display": "Lung Non-small Cell Carcinoma", + "system": "https://disease-ontology.org" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "A (Validated association)" } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae8f5", + "identifier": [ + { + "system": "https://civicdb.org/evidence", + "value": "3017" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae580", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -305,36 +274,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:3908", - "display": "Lung Non-small Cell Carcinoma" + "code": "1424911", + "display": "Dabrafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -343,80 +304,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:3908", + "display": "Lung Non-small Cell Carcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Supports Resistance" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae561", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "91" }, { - "system": "https://civicdb.org/evidence", - "value": "5958" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae8f5", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -424,36 +393,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:3908", - "display": "Lung Non-small Cell Carcinoma" + "code": "NC_000007.14", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -462,32 +423,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "text": "A (Validated association)" - } + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "T" + }, + { + "code": { + "coding": [ + { + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" + "code": "NC_000007.14:140753335:A:T", + "display": "NC_000007.14:140753335:A:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -496,48 +467,77 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 140753335 + } + } + }, + { + "code": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 3.97994e-06 } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "3017" - } - ] + "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/CA12345" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_tx_implications/6.json b/tests/expected_outputs/find_subject_tx_implications/6.json index a4329ef20..cd16a7589 100644 --- a/tests/expected_outputs/find_subject_tx_implications/6.json +++ b/tests/expected_outputs/find_subject_tx_implications/6.json @@ -1,23 +1,14 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "implication", "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae55e", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -25,36 +16,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "", + "display": "Dactolisib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -63,32 +46,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "coding": [ + { + "code": "", + "display": "GDC-0879", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" } ] } @@ -97,46 +86,68 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "text": "D (Preclinical evidence)" + } + }, + { + "code": { + "coding": [ + { "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Does Not Support Resistance" + "text": "Supports Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae902", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1428" }, { - "system": "https://civicdb.org/evidence", - "value": "86" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-58a39ad867e146f585bb553bb10ce85a", + ], "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -144,21 +155,8 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -167,17 +165,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "48013-7", - "display": "Genomic reference sequence ID" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000007.14" + "code": "", + "display": "Dactolisib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -186,18 +185,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000007.14:140753335:A:T", - "display": "NC_000007.14:140753335:A:T" + "code": "2289380", + "display": "Selumetinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -206,98 +205,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, - "valueString": "A" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" - } - ] + "text": "D (Preclinical evidence)" } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "valueRange": { - "low": { - "value": 140753335 - } + "valueCodeableConcept": { + "text": "Supports Sensitivity/Response" } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae901", + "identifier": [ + { + "system": "https://civicdb.org/evidence", + "value": "1005" }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" - } - ] - }, - "valueQuantity": { - "value": 3.97994e-06, - "system": "http://unitsofmeasure.org", - "code": "1" - } + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae55f", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -305,36 +294,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "", + "display": "FOLFOX-4 Regimen", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -343,80 +324,108 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "coding": [ + { + "code": "318341", + "display": "Cetuximab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "Mirdametinib" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] + }, + "valueCodeableConcept": { + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Does Not Support Resistance" + "text": "Supports Resistance" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae90d", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "3739" }, { - "system": "https://civicdb.org/evidence", - "value": "86" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae560", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -424,36 +433,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "", + "display": "MEK Inhibitor RO4987655", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -462,80 +463,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "coding": [ + { + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Resistance" + "text": "Does Not Support Resistance" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae567", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "994" }, { - "system": "https://civicdb.org/evidence", - "value": "90" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae561", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -543,36 +552,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:3908", - "display": "Lung Non-small Cell Carcinoma" + "code": "", + "display": "Mirdametinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -581,80 +582,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" - } - ] + "text": "D (Preclinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Resistance" + "text": "Does Not Support Resistance" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae55f", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "86" }, { - "system": "https://civicdb.org/evidence", - "value": "91" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae562", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -662,36 +671,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "", + "display": "Nutlin-3", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -700,43 +701,63 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "coding": [ + { + "code": "", + "display": "PLX4720", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] + }, + "valueCodeableConcept": { + "text": "D (Preclinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -745,35 +766,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae928", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "97" }, { - "system": "https://civicdb.org/evidence", - "value": "99" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae563", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -781,36 +810,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "", + "display": "PLX4720", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -819,80 +840,108 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "", + "display": "Pictilisib Bismesylate", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] + }, + "valueCodeableConcept": { + "text": "D (Preclinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Resistance" + "text": "Supports Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae92e", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "96" }, { - "system": "https://civicdb.org/evidence", - "value": "126" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae564", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -900,36 +949,48 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "", + "display": "Pictilisib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] + } + }, + { + "code": { + "coding": [ + { "code": "81259-4", - "display": "phenotypic treatment context" + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", "code": "DOID:1909", - "display": "Melanoma" + "display": "Melanoma", + "system": "https://disease-ontology.org" } ] } @@ -938,9 +999,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, @@ -952,29 +1013,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "Pictilisib" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -983,35 +1024,43 @@ } } ], - "identifier": [ + "derivedFrom": [ { - "system": "https://civicdb.org/variant", - "value": "12" - }, + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae564", + "identifier": [ { "system": "https://civicdb.org/evidence", "value": "757" + }, + { + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae565", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1019,36 +1068,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -1057,32 +1098,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "1298944", + "display": "Pertuzumab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" + "code": "DOID:80522", + "display": "Thyroid Gland Anaplastic Carcinoma", + "system": "https://disease-ontology.org" } ] } @@ -1091,46 +1138,68 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "text": "C (Case study)" + } + }, + { + "code": { + "coding": [ + { "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Does Not Support Resistance" + "text": "Supports Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae93f", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "5961" }, { - "system": "https://civicdb.org/evidence", - "value": "816" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae566", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1138,36 +1207,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -1176,32 +1237,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "1424911", + "display": "Dabrafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "51963-7", - "display": "medication-assessed" + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "263034", - "display": "Panitumumab" + "code": "1425099", + "display": "Trametinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -1210,46 +1277,88 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "DOID:50626", + "display": "Gastrointestinal Neuroendocrine Tumor", + "system": "https://disease-ontology.org" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "text": "C (Case study)" + } + }, + { + "code": { + "coding": [ + { "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Does Not Support Resistance" + "text": "Supports Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae8f4", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1430" }, { - "system": "https://civicdb.org/evidence", - "value": "816" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae567", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1257,36 +1366,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -1295,80 +1396,108 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "1722365", + "display": "Cobimetinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "MEK Inhibitor RO4987655" + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] + }, + "valueCodeableConcept": { + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Does Not Support Resistance" + "text": "Supports Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae93e", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1421" }, { - "system": "https://civicdb.org/evidence", - "value": "994" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae568", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1376,36 +1505,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:162", - "display": "Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -1414,32 +1535,58 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "coding": [ + { + "code": "194000", + "display": "Capecitabine", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "51963-7", - "display": "medication-assessed" + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1722365", - "display": "Cobimetinib" + "code": "253337", + "display": "Bevacizumab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" } ] } @@ -1448,9 +1595,23 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "text": "D (Preclinical evidence)" + } + }, + { + "code": { + "coding": [ + { "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -1459,35 +1620,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae8d5", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "98" }, { - "system": "https://civicdb.org/evidence", - "value": "1141" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae569", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1495,36 +1664,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -1533,32 +1694,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", "code": "51963-7", - "display": "medication-assessed" + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "263034", + "display": "Panitumumab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -1567,165 +1714,108 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "coding": [ + { + "code": "51499", + "display": "Irinotecan", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } - } - ], - "identifier": [ - { - "system": 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"display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "DOID:4947", + "display": "Cholangiocarcinoma", + "system": "https://disease-ontology.org" } ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": 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"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1733,36 +1823,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -1771,43 +1853,63 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "263034", + "display": "Panitumumab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] + }, + "valueCodeableConcept": { + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -1816,35 +1918,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae93d", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1413" }, { - "system": "https://civicdb.org/evidence", - "value": "1406" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae56c", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1852,36 +1962,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:8923", - "display": "Skin Melanoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -1890,43 +1992,63 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "A (Validated association)" + "coding": [ + { + "code": "263034", + "display": "Panitumumab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] + }, + "valueCodeableConcept": { + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -1935,35 +2057,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae92a", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1589" }, { - "system": "https://civicdb.org/evidence", - "value": "1409" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae56d", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1971,36 +2101,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:8923", - "display": "Skin Melanoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -2009,43 +2131,83 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "318341", + "display": "Cetuximab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "51963-7", - "display": "medication-assessed" + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "328134", + "display": "Gefitinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] + }, + "valueCodeableConcept": { + "text": "D (Preclinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2054,35 +2216,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae8dc", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1408" }, { - "system": "https://civicdb.org/evidence", - "value": "1410" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae56e", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2090,36 +2260,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:3969", - "display": "Thyroid Gland Papillary Carcinoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -2128,43 +2290,83 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "318341", + "display": "Cetuximab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "51963-7", - "display": "medication-assessed" + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "51499", + "display": "Irinotecan", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] + }, + "valueCodeableConcept": { + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2173,35 +2375,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae917", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1902" }, { - "system": "https://civicdb.org/evidence", - "value": "1414" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae56f", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2209,36 +2419,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:285", - "display": "Hairy Cell Leukemia" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -2247,43 +2449,83 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "318341", + "display": "Cetuximab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "51963-7", - "display": "medication-assessed" + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "51499", + "display": "Irinotecan", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] + }, + "valueCodeableConcept": { + "text": "D (Preclinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2292,35 +2534,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae919", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "8506" }, { - "system": "https://civicdb.org/evidence", - "value": "1579" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae570", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2328,36 +2578,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:3969", - "display": "Thyroid Gland Papillary Carcinoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -2366,43 +2608,63 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "337525", + "display": "Erlotinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] + }, + "valueCodeableConcept": { + "text": "D (Preclinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2411,35 +2673,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae940", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "8507" }, { - "system": "https://civicdb.org/evidence", - "value": "1591" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae572", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2447,36 +2717,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9538", - "display": "Multiple Myeloma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -2485,43 +2747,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2530,35 +2792,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae569", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1398" }, { - "system": "https://civicdb.org/evidence", - "value": "1698" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae573", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2566,36 +2836,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9538", - "display": "Multiple Myeloma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -2604,43 +2866,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2649,35 +2911,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae574", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1749" }, { - "system": "https://civicdb.org/evidence", - "value": "1699" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae574", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2685,36 +2955,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -2723,43 +2985,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -2768,35 +3030,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae57a", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "3750" }, { - "system": "https://civicdb.org/evidence", - "value": "1749" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae575", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2804,36 +3074,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -2842,80 +3104,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "263034", - "display": "Panitumumab" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Resistance" + "text": "Supports Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae57b", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "3755" }, { - "system": "https://civicdb.org/evidence", - "value": "2115" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae576", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2923,36 +3193,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -2961,80 +3223,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Resistance" + "text": "Supports Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae57c", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "3757" }, { - "system": "https://civicdb.org/evidence", - "value": "2115" - } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae577", + "system": "https://civicdb.org/variant", + "value": "12" + } + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3042,36 +3312,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -3080,43 +3342,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "32592", - "display": "Oxaliplatin" - } - ] + "text": "D (Preclinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -3125,35 +3387,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae560", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "90" }, { - "system": "https://civicdb.org/evidence", - "value": "2117" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae578", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3161,36 +3431,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -3199,80 +3461,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:2394", + "display": "Ovarian Cancer", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "51499", - "display": "Irinotecan" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Resistance" + "text": "Supports Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae581", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "5959" }, { - "system": "https://civicdb.org/evidence", - "value": "2118" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae579", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3280,36 +3550,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -3318,43 +3580,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:285", + "display": "Hairy Cell Leukemia", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -3363,35 +3625,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae56f", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1579" }, { - "system": "https://civicdb.org/evidence", - "value": "2135" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae57a", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3399,36 +3669,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -3437,43 +3699,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:2876", + "display": "Laryngeal Squamous Cell Carcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -3482,72 +3744,72 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae583", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "5962" }, { - "system": "https://civicdb.org/evidence", - "value": "3750" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae57b", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } ], "code": { "coding": [ - { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" - } - ] - }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], + { + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" + } + ] + }, "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -3556,43 +3818,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:3908", + "display": "Lung Non-small Cell Carcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -3601,35 +3863,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae580", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "5958" }, { - "system": "https://civicdb.org/evidence", - "value": "3755" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae57c", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3637,36 +3907,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -3675,43 +3937,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:3969", + "display": "Thyroid Gland Papillary Carcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -3720,35 +3982,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae570", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1591" }, { - "system": "https://civicdb.org/evidence", - "value": "3757" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae57d", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3756,36 +4026,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:6812", - "display": "Childhood Pilocytic Astrocytoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -3794,43 +4056,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:3969", + "display": "Thyroid Gland Papillary Carcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -3839,35 +4101,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae58a", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "9018" }, { - "system": "https://civicdb.org/evidence", - "value": "3777" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae57e", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3875,36 +4145,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:50933", - "display": "Ovarian Serous Carcinoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -3913,43 +4175,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:3969", + "display": "Thyroid Gland Papillary Carcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -3958,35 +4220,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae56e", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1414" }, { - "system": "https://civicdb.org/evidence", - "value": "3787" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae57f", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3994,36 +4264,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -4032,80 +4294,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:50933", + "display": "Ovarian Serous Carcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "263034", - "display": "Panitumumab" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Resistance" + "text": "Supports Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae57e", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "3787" }, { - "system": "https://civicdb.org/evidence", - "value": "3827" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae580", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4113,36 +4383,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:3908", - "display": "Lung Non-small Cell Carcinoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -4151,43 +4413,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:6812", + "display": "Childhood Pilocytic Astrocytoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -4196,35 +4458,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae57d", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "3777" }, { - "system": "https://civicdb.org/evidence", - "value": "5958" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae581", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4232,36 +4502,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:2394", - "display": "Ovarian Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -4270,43 +4532,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:7146", + "display": "Langerhans Cell Sarcoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -4315,35 +4577,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae589", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "7583" }, { - "system": "https://civicdb.org/evidence", - "value": "5959" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae582", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4351,36 +4621,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -4389,43 +4651,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:80522", + "display": "Thyroid Gland Anaplastic Carcinoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -4434,35 +4696,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae588", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "6045" }, { - "system": "https://civicdb.org/evidence", - "value": "5960" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae583", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4470,36 +4740,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:2876", - "display": "Laryngeal Squamous Cell Carcinoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -4508,43 +4770,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "DOID:8923", + "display": "Skin Melanoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "A (Validated association)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -4553,35 +4815,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae56c", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1409" }, { - "system": "https://civicdb.org/evidence", - "value": "5962" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae588", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4589,36 +4859,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:80522", - "display": "Thyroid Gland Anaplastic Carcinoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -4627,43 +4889,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:8923", + "display": "Skin Melanoma", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -4672,35 +4934,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae56d", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1410" }, { - "system": "https://civicdb.org/evidence", - "value": "6045" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae589", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4708,36 +4978,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:7146", - "display": "Langerhans Cell Sarcoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -4746,80 +5008,88 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Does Not Support Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae56a", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1405" }, { - "system": "https://civicdb.org/evidence", - "value": "7583" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae58a", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4827,36 +5097,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:3969", - "display": "Thyroid Gland Papillary Carcinoma" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -4865,43 +5127,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -4910,35 +5172,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae582", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "5960" }, { - "system": "https://civicdb.org/evidence", - "value": "9018" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae8d3", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -4946,70 +5216,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", "code": "51963-7", - "display": "medication-assessed" + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "2049122", - "display": "Binimetinib" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -5018,18 +5246,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" } ] } @@ -5038,29 +5266,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "2049106", - "display": "Encorafenib" - } - ] + "text": "D (Preclinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -5069,35 +5291,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae562", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "99" }, { - "system": "https://civicdb.org/evidence", - "value": "7612" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae8d5", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5105,70 +5335,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "D (Preclinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", "code": "51963-7", - "display": "medication-assessed" + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "194000", - "display": "Capecitabine" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -5177,18 +5365,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "253337", - "display": "Bevacizumab" + "code": "DOID:9538", + "display": "Multiple Myeloma", + "system": "https://disease-ontology.org" } ] } @@ -5197,29 +5385,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -5228,35 +5410,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae572", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1698" }, { - "system": "https://civicdb.org/evidence", - "value": "98" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae8dc", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5264,70 +5454,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "D (Preclinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", "code": "51963-7", - "display": "medication-assessed" + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" + "code": "1147220", + "display": "Vemurafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -5336,18 +5484,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "328134", - "display": "Gefitinib" + "code": "DOID:9538", + "display": "Multiple Myeloma", + "system": "https://disease-ontology.org" } ] } @@ -5356,29 +5504,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -5387,35 +5529,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae573", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1699" }, { - "system": "https://civicdb.org/evidence", - "value": "1408" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae8f4", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5423,36 +5573,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:50626", - "display": "Gastrointestinal Neuroendocrine Tumor" + "code": "1424911", + "display": "Dabrafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -5461,32 +5603,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "1425099", + "display": "Trametinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "51963-7", - "display": "medication-assessed" + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" + "code": "263034", + "display": "Panitumumab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -5495,18 +5643,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" } ] } @@ -5515,29 +5663,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -5546,35 +5688,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae92b", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "6123" }, { - "system": "https://civicdb.org/evidence", - "value": "1430" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae8f5", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5582,36 +5732,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:3908", - "display": "Lung Non-small Cell Carcinoma" + "code": "1424911", + "display": "Dabrafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -5620,32 +5762,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "A (Validated association)" + "coding": [ + { + "code": "1425099", + "display": "Trametinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" } ] } @@ -5654,29 +5802,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -5685,35 +5827,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae8fa", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "6178" }, { - "system": "https://civicdb.org/evidence", - "value": "3017" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae8f6", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5721,36 +5871,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:8923", - "display": "Skin Melanoma" + "code": "1424911", + "display": "Dabrafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -5759,32 +5901,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "1425099", + "display": "Trametinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" } ] } @@ -5793,29 +5941,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -5824,35 +5966,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae8fb", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "6940" }, { - "system": "https://civicdb.org/evidence", - "value": "3758" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae8f7", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5860,36 +6010,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:4947", - "display": "Cholangiocarcinoma" + "code": "1424911", + "display": "Dabrafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -5898,32 +6040,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "1425099", + "display": "Trametinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" } ] } @@ -5932,29 +6080,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -5963,35 +6105,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae8fd", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "95" }, { - "system": "https://civicdb.org/evidence", - "value": "5902" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae8f8", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -5999,36 +6149,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:4928", - "display": "Intrahepatic Cholangiocarcinoma" + "code": "1424911", + "display": "Dabrafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -6037,32 +6179,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "1425099", + "display": "Trametinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" } ] } @@ -6071,29 +6219,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -6102,35 +6244,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae938", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "6938" }, { - "system": "https://civicdb.org/evidence", - "value": "5903" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae8f9", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6138,36 +6288,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:4928", - "display": "Intrahepatic Cholangiocarcinoma" + "code": "1424911", + "display": "Dabrafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -6176,32 +6318,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "1425099", + "display": "Trametinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" + "code": "DOID:3908", + "display": "Lung Non-small Cell Carcinoma", + "system": "https://disease-ontology.org" } ] } @@ -6210,29 +6358,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] + "valueCodeableConcept": { + "text": "A (Validated association)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -6241,35 +6383,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae8f5", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "3017" }, { - "system": "https://civicdb.org/evidence", - "value": "5904" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae8fa", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6277,36 +6427,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "1424911", + "display": "Dabrafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -6315,32 +6457,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "1425099", + "display": "Trametinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" + "code": "DOID:4607", + "display": "Biliary Tract Cancer", + "system": "https://disease-ontology.org" } ] } @@ -6349,29 +6497,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -6380,35 +6522,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae8fc", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "7264" }, { - "system": "https://civicdb.org/evidence", - "value": "6178" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae8fb", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6416,36 +6566,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "1424911", + "display": "Dabrafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -6454,32 +6596,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "1425099", + "display": "Trametinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" + "code": "DOID:4928", + "display": "Intrahepatic Cholangiocarcinoma", + "system": "https://disease-ontology.org" } ] } @@ -6488,29 +6636,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -6519,35 +6661,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae8f8", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "5903" }, { - "system": "https://civicdb.org/evidence", - "value": "6940" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae8fc", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6555,36 +6705,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:4607", - "display": "Biliary Tract Cancer" + "code": "1424911", + "display": "Dabrafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -6593,32 +6735,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "1425099", + "display": "Trametinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" + "code": "DOID:4928", + "display": "Intrahepatic Cholangiocarcinoma", + "system": "https://disease-ontology.org" } ] } @@ -6627,29 +6775,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -6658,35 +6800,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae8f9", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "5904" }, { - "system": "https://civicdb.org/evidence", - "value": "7264" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae8fd", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6694,36 +6844,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "1424911", + "display": "Dabrafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -6732,32 +6874,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "1425099", + "display": "Trametinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" + "code": "DOID:4947", + "display": "Cholangiocarcinoma", + "system": "https://disease-ontology.org" } ] } @@ -6766,29 +6914,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -6797,35 +6939,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae8f7", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "5902" }, { - "system": "https://civicdb.org/evidence", - "value": "95" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae901", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6833,36 +6983,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" + "code": "1424911", + "display": "Dabrafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -6871,32 +7013,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "coding": [ + { + "code": "1425099", + "display": "Trametinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "Dactolisib" + "code": "DOID:80522", + "display": "Thyroid Gland Anaplastic Carcinoma", + "system": "https://disease-ontology.org" } ] } @@ -6905,29 +7053,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "2289380", - "display": "Selumetinib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -6936,35 +7078,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae939", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "6975" }, { - "system": "https://civicdb.org/evidence", - "value": "1005" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae902", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -6972,36 +7122,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1424911", + "display": "Dabrafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -7010,32 +7152,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "coding": [ + { + "code": "1425099", + "display": "Trametinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "Dactolisib" + "code": "DOID:8923", + "display": "Skin Melanoma", + "system": "https://disease-ontology.org" } ] } @@ -7044,29 +7192,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "GDC-0879" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -7075,35 +7217,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae8f6", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "3758" }, { - "system": "https://civicdb.org/evidence", - "value": "1428" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae907", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7111,70 +7261,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", "code": "51963-7", - "display": "medication-assessed" + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "2049106", - "display": "Encorafenib" + "code": "1424911", + "display": "Dabrafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -7183,18 +7291,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "2049122", - "display": "Binimetinib" + "code": "DOID:3908", + "display": "Lung Non-small Cell Carcinoma", + "system": "https://disease-ontology.org" } ] } @@ -7203,66 +7311,68 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Supports Resistance" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae561", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "91" }, { - "system": "https://civicdb.org/evidence", - "value": "7260" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae908", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7270,70 +7380,48 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "1424911", + "display": "Dabrafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] - }, - "valueCodeableConcept": { - "text": "A (Validated association)" } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "2049106", - "display": "Encorafenib" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" } ] } @@ -7342,66 +7430,68 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Does Not Support Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae56b", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1406" }, { - "system": "https://civicdb.org/evidence", - "value": "9851" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae90d", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7409,36 +7499,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "1425099", + "display": "Trametinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -7447,32 +7529,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "263034", + "display": "Panitumumab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "FOLFOX-4 Regimen" + "code": "DOID:50861", + "display": "Colorectal Adenocarcinoma", + "system": "https://disease-ontology.org" } ] } @@ -7481,66 +7569,68 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Resistance" + "text": "Does Not Support Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae92c", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "6124" }, { - "system": "https://civicdb.org/evidence", - "value": "3739" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae917", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7548,70 +7638,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" - } - ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", "code": "51963-7", - "display": "medication-assessed" + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "51499", - "display": "Irinotecan" + "code": "1425099", + "display": "Trametinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -7620,18 +7668,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" } ] } @@ -7640,29 +7688,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -7671,35 +7713,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae579", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "2135" }, { - "system": "https://civicdb.org/evidence", - "value": "1902" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae918", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7707,36 +7757,48 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "1425099", + "display": "Trametinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] + } + }, + { + "code": { + "coding": [ + { "code": "81259-4", - "display": "phenotypic treatment context" + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:4947", - "display": "Cholangiocarcinoma" + "code": "DOID:1909", + "display": "Melanoma", + "system": "https://disease-ontology.org" } ] } @@ -7745,32 +7807,97 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "93044-6", - "display": "Level of evidence" + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "text": "D (Preclinical evidence)" + } + }, + { + "code": { + "coding": [ + { + "code": "predicted-therapeutic-implication", + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" + } + ] + }, + "valueCodeableConcept": { + "text": "Does Not Support Resistance" + } + } + ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae55e", + "identifier": [ + { + "system": "https://civicdb.org/evidence", + "value": "86" + }, + { + "system": "https://civicdb.org/variant", + "value": "12" + } + ], + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } - }, + ] + }, + "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", "code": "51963-7", - "display": "medication-assessed" + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "51499", - "display": "Irinotecan" + "code": "1722365", + "display": "Cobimetinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -7779,18 +7906,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "DOID:162", + "display": "Cancer", + "system": "https://disease-ontology.org" } ] } @@ -7799,29 +7926,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "263034", - "display": "Panitumumab" - } - ] + "text": "D (Preclinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -7830,35 +7951,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae568", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "1141" }, { - "system": "https://civicdb.org/evidence", - "value": "5906" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae919", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -7866,36 +7995,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "194000", + "display": "Capecitabine", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -7904,32 +8025,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "coding": [ + { + "code": "253337", + "display": "Bevacizumab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "51963-7", - "display": "medication-assessed" + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "51499", - "display": "Irinotecan" + "code": "32592", + "display": "Oxaliplatin", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -7938,18 +8065,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" } ] } @@ -7958,66 +8085,68 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "318341", - "display": "Cetuximab" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Supports Resistance" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae929", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "2121" }, { - "system": "https://civicdb.org/evidence", - "value": "8506" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae928", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8025,36 +8154,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "2049106", + "display": "Encorafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -8063,32 +8184,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "D (Preclinical evidence)" + "coding": [ + { + "code": "2049122", + "display": "Binimetinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "51963-7", - "display": "medication-assessed" + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "Nutlin-3" + "code": "318341", + "display": "Cetuximab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -8097,29 +8224,43 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "PLX4720" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" + } + ] + } + }, + { + "code": { + "coding": [ + { + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] + }, + "valueCodeableConcept": { + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -8128,35 +8269,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae8d3", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "7612" }, { - "system": "https://civicdb.org/evidence", - "value": "97" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae929", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8164,36 +8313,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "2049106", + "display": "Encorafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -8202,32 +8343,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "B (Clinical evidence)" + "coding": [ + { + "code": "2049122", + "display": "Binimetinib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "51963-7", - "display": "medication-assessed" + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "32592", - "display": "Oxaliplatin" + "code": "318341", + "display": "Cetuximab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -8236,18 +8383,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "194000", - "display": "Capecitabine" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" } ] } @@ -8256,66 +8403,68 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "253337", - "display": "Bevacizumab" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Resistance" + "text": "Supports Sensitivity/Response" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae907", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "7260" }, { - "system": "https://civicdb.org/evidence", - "value": "2121" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae92a", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8323,36 +8472,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "2049106", + "display": "Encorafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -8361,32 +8502,38 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "C (Case study)" + "coding": [ + { + "code": "318341", + "display": "Cetuximab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "263034", - "display": "Panitumumab" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" } ] } @@ -8395,29 +8542,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" - } - ] + "text": "A (Validated association)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -8426,35 +8567,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae908", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "9851" }, { - "system": "https://civicdb.org/evidence", - "value": "1589" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae92b", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8462,70 +8611,48 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "263034", + "display": "Panitumumab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "51963-7", - "display": "medication-assessed" + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "263034", - "display": "Panitumumab" + "code": "495881", + "display": "Sorafenib", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] } @@ -8534,18 +8661,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" } ] } @@ -8554,29 +8681,23 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" - } - ] + "text": "D (Preclinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, @@ -8585,35 +8706,43 @@ } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae935", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "89" }, { - "system": "https://civicdb.org/evidence", - "value": "6123" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae92c", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8621,70 +8750,48 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:50861", - "display": "Colorectal Adenocarcinoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "263034", + "display": "Panitumumab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "263034", - "display": "Panitumumab" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" } ] } @@ -8693,66 +8800,68 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Does Not Support Sensitivity/Response" + "text": "Does Not Support Resistance" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae566", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "816" }, { - "system": "https://civicdb.org/evidence", - "value": "6124" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae92e", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8760,70 +8869,48 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "263034", + "display": "Panitumumab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] - }, - "valueCodeableConcept": { - "text": "D (Preclinical evidence)" } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "Pictilisib Bismesylate" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" } ] } @@ -8832,66 +8919,68 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "", - "display": "PLX4720" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Supports Resistance" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae575", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "2115" }, { - "system": "https://civicdb.org/evidence", - "value": "96" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae935", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -8899,70 +8988,48 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "263034", + "display": "Panitumumab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] - }, - "valueCodeableConcept": { - "text": "D (Preclinical evidence)" } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "495881", - "display": "Sorafenib" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" } ] } @@ -8971,66 +9038,68 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "263034", - "display": "Panitumumab" - } - ] + "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Supports Resistance" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae57f", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "3827" }, { - "system": "https://civicdb.org/evidence", - "value": "89" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae938", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -9038,70 +9107,48 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "318341", + "display": "Cetuximab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" } ] } @@ -9110,66 +9157,68 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Does Not Support Resistance" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae565", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "816" }, { - "system": "https://civicdb.org/evidence", - "value": "6938" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae939", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -9177,70 +9226,48 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:80522", - "display": "Thyroid Gland Anaplastic Carcinoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "318341", + "display": "Cetuximab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1425099", - "display": "Trametinib" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" } ] } @@ -9249,66 +9276,68 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1424911", - "display": "Dabrafenib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Supports Resistance" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae563", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "126" }, { - "system": "https://civicdb.org/evidence", - "value": "6975" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae93d", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -9316,138 +9345,118 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "318341", + "display": "Cetuximab", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" } ] } }, { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" - } - ] - }, - "valueCodeableConcept": { + "code": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "263034", - "display": "Panitumumab" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] + }, + "valueCodeableConcept": { + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Does Not Support Sensitivity/Response" + "text": "Supports Resistance" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae576", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "2115" }, { - "system": "https://civicdb.org/evidence", - "value": "1413" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae93e", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -9455,70 +9464,48 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:1909", - "display": "Melanoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "32592", + "display": "Oxaliplatin", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] - }, - "valueCodeableConcept": { - "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" } ] } @@ -9527,66 +9514,68 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1722365", - "display": "Cobimetinib" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Supports Resistance" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae577", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "2117" }, { - "system": "https://civicdb.org/evidence", - "value": "1421" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae93f", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "implication", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -9594,70 +9583,48 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "51963-7", + "display": "medication-assessed", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:80522", - "display": "Thyroid Gland Anaplastic Carcinoma" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "51499", + "display": "Irinotecan", + "system": "http://www.nlm.nih.gov/research/umls/rxnorm" } ] - }, - "valueCodeableConcept": { - "text": "C (Case study)" } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81259-4", + "display": "phenotypic treatment context", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "DOID:9256", + "display": "Colorectal Cancer", + "system": "https://disease-ontology.org" } ] } @@ -9666,66 +9633,68 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "93044-6", + "display": "Level of evidence", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "coding": [ - { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1298944", - "display": "Pertuzumab" - } - ] + "text": "B (Clinical evidence)" } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "display": "predicted-therapeutic-implication", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "text": "Supports Resistance" } } ], + "derivedFrom": [ + { + "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" + } + ], + "id": "dv-6737a82bd7c0d2714e4ae578", "identifier": [ { - "system": "https://civicdb.org/variant", - "value": "12" + "system": "https://civicdb.org/evidence", + "value": "2118" }, { - "system": "https://civicdb.org/evidence", - "value": "5961" + "system": "https://civicdb.org/variant", + "value": "12" } - ] - } - }, - { - "name": "implication", - "resource": { - "resourceType": "Observation", - "id": "dv-6737a82bd7c0d2714e4ae940", + ], "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/CA12345" + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -9733,36 +9702,28 @@ "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "therapeutic-implication" + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, - "subject": { - "reference": "Patient/CA12345" - }, - "derivedFrom": [ - { - "reference": "Observation/dv-58a39ad867e146f585bb553bb10ce85a" - } - ], "component": [ { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81259-4", - "display": "phenotypic treatment context" + "code": "48013-7", + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://disease-ontology.org", - "code": "DOID:9256", - "display": "Colorectal Cancer" + "code": "NC_000007.14", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -9771,32 +9732,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "93044-6", - "display": "Level of evidence" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "text": "D (Preclinical evidence)" - } + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "T" + }, + { + "code": { + "coding": [ + { + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "1147220", - "display": "Vemurafenib" + "code": "NC_000007.14:140753335:A:T", + "display": "NC_000007.14:140753335:A:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -9805,48 +9776,77 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "51963-7", - "display": "medication-assessed" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 140753335 + } + } + }, + { + "code": { "coding": [ { - "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - "code": "337525", - "display": "Erlotinib" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 3.97994e-06 } }, { "code": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", - "code": "predicted-therapeutic-implication", - "display": "predicted-therapeutic-implication" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { - "text": "Supports Sensitivity/Response" + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } ], - "identifier": [ - { - "system": "https://civicdb.org/variant", - "value": "12" - }, - { - "system": "https://civicdb.org/evidence", - "value": "8507" - } - ] + "id": "dv-58a39ad867e146f585bb553bb10ce85a", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/CA12345" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_variants/1.json b/tests/expected_outputs/find_subject_variants/1.json index b030ddaff..930d8caa8 100644 --- a/tests/expected_outputs/find_subject_variants/1.json +++ b/tests/expected_outputs/find_subject_variants/1.json @@ -1,34 +1,25 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ - { - "name": "rangeItem", - "valueString": "NC_000019.10:11089431-11133820" - }, { "name": "presence", "valueBoolean": true }, + { + "name": "rangeItem", + "valueString": "NC_000019.10:11089431-11133820" + }, { "name": "variant", "resource": { - "resourceType": "Observation", - "id": "dv-0cbf052b7dc2453c83798496893eeb8a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -36,21 +27,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -59,18 +38,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -79,17 +58,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -98,18 +77,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6705-3", - "display": "homozygous" + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -118,18 +97,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "A" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, + { + "code": { + "coding": [ + { "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243253:T:C", - "display": "NC_000019.9:11243253:T:C" + "code": "NC_000019.9:11233940:A:G", + "display": "NC_000019.9:11233940:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -138,99 +141,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 11233940 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.781146 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243253 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-24497150208846dbbb94cf13157d76d1", + ], + "id": "dv-3f58c03ccc244f01820bf9445e076d69", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -238,21 +245,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -261,18 +256,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -281,17 +276,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -300,18 +295,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -320,119 +315,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "AC" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243331:C:A", - "display": "NC_000019.9:11243331:C:A" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "AAG" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243208:C:AG", + "display": "NC_000019.9:11243208:C:AG", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueRange": { + "low": { + "value": 11243207 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243331 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-25751058304a4b40a5254642589509ae", + ], + "id": "dv-9911e411d71f41789c58a251995db6ab", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -440,21 +447,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -463,18 +458,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -483,17 +478,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -502,18 +497,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -522,18 +517,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "C" + }, + { + "code": { + "coding": [ + { "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242495:G:A", - "display": "NC_000019.9:11242495:G:A" + "code": "NC_000019.9:11242306:G:C", + "display": "NC_000019.9:11242306:G:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -542,99 +561,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 11242306 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.818994 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11242495 - } - } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-3bd5a669b6b14313bb6585f4f0249b8e", + ], + "id": "dv-904b6ac36b25461ea7a2304093bc6fec", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -642,21 +665,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -665,18 +676,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -685,17 +696,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -704,18 +715,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -724,119 +735,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "T" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243367:T:C", - "display": "NC_000019.9:11243367:T:C" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11242657:T:C", + "display": "NC_000019.9:11242657:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueRange": { + "low": { + "value": 11242657 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243367 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-3f58c03ccc244f01820bf9445e076d69", + ], + "id": "dv-57370e44f9884d8cb43661abf73c23c3", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -844,21 +867,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -867,18 +878,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -887,17 +898,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -906,99 +917,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11233940:A:G", - "display": "NC_000019.9:11233940:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "display": "homozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.9:11243253:T:C", + "display": "NC_000019.9:11243253:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -1007,15 +981,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 11233940 + "value": 11243253 } } }, @@ -1023,38 +997,71 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.781146, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-40f05bda5c564d8bb5d775df91b83873", + ], + "id": "dv-0cbf052b7dc2453c83798496893eeb8a", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1062,21 +1069,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -1085,18 +1080,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -1105,17 +1100,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -1124,18 +1119,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -1144,119 +1139,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243259:C:T", - "display": "NC_000019.9:11243259:C:T" - } - ] - } + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueString": "C" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "NC_000019.9:11242764:A:G", + "display": "NC_000019.9:11242764:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 11242764 + } + } + }, + { + "code": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 11243259 - } + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-46597e63d927405d8818e0867d0e521c", + ], + "id": "dv-930a27aa386d4cb8bff1e437040afb45", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1264,21 +1271,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -1287,18 +1282,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -1307,17 +1302,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -1326,99 +1321,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11210927:C:T", - "display": "NC_000019.9:11210927:C:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.9:11243444:A:G", + "display": "NC_000019.9:11243444:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -1427,15 +1385,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 11210927 + "value": 11243444 } } }, @@ -1443,38 +1401,71 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 7.96318e-06, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", + ], "id": "dv-47e65009ae414a218cf7efe34f83c3e0", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1482,21 +1473,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -1505,18 +1484,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -1525,17 +1504,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -1544,18 +1523,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -1564,119 +1543,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "C" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243444:A:G", - "display": "NC_000019.9:11243444:A:G" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243331:C:A", + "display": "NC_000019.9:11243331:C:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueRange": { + "low": { + "value": 11243331 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243444 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-5459aa2045a740c0af8c14cbc66cd4f2", + ], + "id": "dv-24497150208846dbbb94cf13157d76d1", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1684,21 +1675,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -1707,18 +1686,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -1727,17 +1706,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -1746,18 +1725,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -1766,119 +1745,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243501:T:C", - "display": "NC_000019.9:11243501:T:C" - } - ] - } + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueString": "T" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "NC_000019.9:11243327:C:G", + "display": "NC_000019.9:11243327:C:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 11243327 + } + } + }, + { + "code": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 11243501 - } + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-57370e44f9884d8cb43661abf73c23c3", + ], + "id": "dv-9ad6695f56dd4d82afb319c8331d3a6d", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1886,21 +1877,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -1909,18 +1888,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -1929,17 +1908,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -1948,18 +1927,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -1968,18 +1947,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "C" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "T" + }, + { + "code": { + "coding": [ + { "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242657:T:C", - "display": "NC_000019.9:11242657:T:C" + "code": "NC_000019.9:11210927:C:T", + "display": "NC_000019.9:11210927:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -1988,99 +1991,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 11210927 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 7.96318e-06 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11242657 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-7811771c3f3344dca8b4fcf0f9fd84b1", + ], + "id": "dv-46597e63d927405d8818e0867d0e521c", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2088,21 +2095,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -2111,18 +2106,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -2131,17 +2126,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -2150,18 +2145,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -2170,119 +2165,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "C" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243591:G:T", - "display": "NC_000019.9:11243591:G:T" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243259:C:T", + "display": "NC_000019.9:11243259:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueRange": { + "low": { + "value": 11243259 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243591 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-904b6ac36b25461ea7a2304093bc6fec", + ], + "id": "dv-40f05bda5c564d8bb5d775df91b83873", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2290,21 +2297,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -2313,18 +2308,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -2333,17 +2328,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -2352,18 +2347,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -2372,79 +2367,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242306:G:C", - "display": "NC_000019.9:11242306:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.9:11243734:C:T", + "display": "NC_000019.9:11243734:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -2453,15 +2411,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 11242306 + "value": 11243734 } } }, @@ -2469,38 +2427,71 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.818994, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-930a27aa386d4cb8bff1e437040afb45", + ], + "id": "dv-a4bc1ce389c943248c967f087971ba88", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2508,21 +2499,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -2531,18 +2510,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -2551,17 +2530,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -2570,18 +2549,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -2590,18 +2569,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "A" + }, + { + "code": { + "coding": [ + { "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242764:A:G", - "display": "NC_000019.9:11242764:A:G" + "code": "NC_000019.9:11242043:G:A", + "display": "NC_000019.9:11242043:G:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -2610,99 +2613,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 11242043 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.243375 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11242764 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-9911e411d71f41789c58a251995db6ab", + ], + "id": "dv-ec3a667068394825be063d587250d6e2", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2710,21 +2717,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -2733,18 +2728,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -2753,17 +2748,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -2772,18 +2767,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -2792,119 +2787,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "G" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243208:C:AG", - "display": "NC_000019.9:11243208:C:AG" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11242495:G:A", + "display": "NC_000019.9:11242495:G:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "AC" + "valueRange": { + "low": { + "value": 11242495 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "AAG" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11243207 - } - } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-9ad6695f56dd4d82afb319c8331d3a6d", + ], + "id": "dv-25751058304a4b40a5254642589509ae", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2912,21 +2919,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -2935,18 +2930,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -2955,17 +2950,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -2974,18 +2969,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -2994,119 +2989,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "G" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243327:C:G", - "display": "NC_000019.9:11243327:C:G" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243159:G:A", + "display": "NC_000019.9:11243159:G:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueRange": { + "low": { + "value": 11243159 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243327 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-a4bc1ce389c943248c967f087971ba88", + ], + "id": "dv-ae2c1cd27dd44fb79b1b949e56ae7833", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3114,21 +3121,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -3137,18 +3132,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -3157,17 +3152,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -3176,18 +3171,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -3196,141 +3191,141 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "G" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243734:C:T", - "display": "NC_000019.9:11243734:C:T" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243591:G:T", + "display": "NC_000019.9:11243591:G:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueRange": { + "low": { + "value": 11243591 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243734 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-ae2c1cd27dd44fb79b1b949e56ae7833", + ], + "id": "dv-7811771c3f3344dca8b4fcf0f9fd84b1", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, "subject": { "reference": "Patient/HG00403" }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -3339,18 +3334,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -3359,17 +3354,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -3378,18 +3373,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -3398,119 +3393,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "T" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243159:G:A", - "display": "NC_000019.9:11243159:G:A" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243367:T:C", + "display": "NC_000019.9:11243367:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueRange": { + "low": { + "value": 11243367 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243159 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-d5e6a6a584a44454901740ac1d9c4b1f", + ], + "id": "dv-3bd5a669b6b14313bb6585f4f0249b8e", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3518,21 +3525,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -3541,18 +3536,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -3561,17 +3556,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -3580,18 +3575,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -3600,119 +3595,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "T" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243223:CTACTA:CTA", - "display": "NC_000019.9:11243223:CTACTA:CTA" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243501:T:C", + "display": "NC_000019.9:11243501:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "TCTA" + "valueRange": { + "low": { + "value": 11243501 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243222 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-ec3a667068394825be063d587250d6e2", + ], + "id": "dv-5459aa2045a740c0af8c14cbc66cd4f2", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3720,21 +3727,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -3743,18 +3738,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -3763,17 +3758,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -3782,99 +3777,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242043:G:A", - "display": "NC_000019.9:11242043:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueString": "TCTA" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.9:11243223:CTACTA:CTA", + "display": "NC_000019.9:11243223:CTACTA:CTA", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -3883,15 +3841,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 11242043 + "value": 11243222 } } }, @@ -3899,22 +3857,64 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.243375, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] + ], + "id": "dv-d5e6a6a584a44454901740ac1d9c4b1f", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_variants/2.json b/tests/expected_outputs/find_subject_variants/2.json index d8f0ec5f8..e13d98e72 100644 --- a/tests/expected_outputs/find_subject_variants/2.json +++ b/tests/expected_outputs/find_subject_variants/2.json @@ -1,34 +1,25 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ - { - "name": "rangeItem", - "valueString": "NC_000019.9:11200138-11244496" - }, { "name": "presence", "valueBoolean": true }, + { + "name": "rangeItem", + "valueString": "NC_000019.9:11200138-11244496" + }, { "name": "variant", "resource": { - "resourceType": "Observation", - "id": "dv-0cbf052b7dc2453c83798496893eeb8a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -36,21 +27,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -59,18 +38,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -79,17 +58,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -98,18 +77,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6705-3", - "display": "homozygous" + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -118,18 +97,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "A" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, + { + "code": { + "coding": [ + { "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243253:T:C", - "display": "NC_000019.9:11243253:T:C" + "code": "NC_000019.9:11233940:A:G", + "display": "NC_000019.9:11233940:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -138,99 +141,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 11233940 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.781146 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243253 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-24497150208846dbbb94cf13157d76d1", + ], + "id": "dv-3f58c03ccc244f01820bf9445e076d69", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -238,21 +245,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -261,18 +256,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -281,17 +276,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -300,18 +295,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -320,119 +315,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "AC" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243331:C:A", - "display": "NC_000019.9:11243331:C:A" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "AAG" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243208:C:AG", + "display": "NC_000019.9:11243208:C:AG", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueRange": { + "low": { + "value": 11243207 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243331 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-25751058304a4b40a5254642589509ae", + ], + "id": "dv-9911e411d71f41789c58a251995db6ab", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -440,21 +447,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -463,18 +458,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -483,17 +478,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -502,18 +497,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -522,18 +517,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "C" + }, + { + "code": { + "coding": [ + { "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242495:G:A", - "display": "NC_000019.9:11242495:G:A" + "code": "NC_000019.9:11242306:G:C", + "display": "NC_000019.9:11242306:G:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -542,99 +561,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 11242306 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.818994 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11242495 - } - } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-3bd5a669b6b14313bb6585f4f0249b8e", + ], + "id": "dv-904b6ac36b25461ea7a2304093bc6fec", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -642,21 +665,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -665,18 +676,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -685,17 +696,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -704,18 +715,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -724,119 +735,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "T" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243367:T:C", - "display": "NC_000019.9:11243367:T:C" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11242657:T:C", + "display": "NC_000019.9:11242657:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueRange": { + "low": { + "value": 11242657 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243367 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-3f58c03ccc244f01820bf9445e076d69", + ], + "id": "dv-57370e44f9884d8cb43661abf73c23c3", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -844,21 +867,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -867,18 +878,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -887,17 +898,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -906,99 +917,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11233940:A:G", - "display": "NC_000019.9:11233940:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "display": "homozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.9:11243253:T:C", + "display": "NC_000019.9:11243253:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -1007,15 +981,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 11233940 + "value": 11243253 } } }, @@ -1023,38 +997,71 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.781146, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-40f05bda5c564d8bb5d775df91b83873", + ], + "id": "dv-0cbf052b7dc2453c83798496893eeb8a", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1062,21 +1069,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -1085,18 +1080,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -1105,17 +1100,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -1124,18 +1119,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -1144,119 +1139,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243259:C:T", - "display": "NC_000019.9:11243259:C:T" - } - ] - } + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueString": "C" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "NC_000019.9:11242764:A:G", + "display": "NC_000019.9:11242764:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 11242764 + } + } + }, + { + "code": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 11243259 - } + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-46597e63d927405d8818e0867d0e521c", + ], + "id": "dv-930a27aa386d4cb8bff1e437040afb45", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1264,21 +1271,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -1287,18 +1282,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -1307,17 +1302,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -1326,99 +1321,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11210927:C:T", - "display": "NC_000019.9:11210927:C:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.9:11243444:A:G", + "display": "NC_000019.9:11243444:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -1427,15 +1385,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 11210927 + "value": 11243444 } } }, @@ -1443,38 +1401,71 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 7.96318e-06, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", + ], "id": "dv-47e65009ae414a218cf7efe34f83c3e0", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1482,21 +1473,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -1505,18 +1484,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -1525,17 +1504,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -1544,18 +1523,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -1564,119 +1543,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "C" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243444:A:G", - "display": "NC_000019.9:11243444:A:G" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243331:C:A", + "display": "NC_000019.9:11243331:C:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueRange": { + "low": { + "value": 11243331 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243444 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-5459aa2045a740c0af8c14cbc66cd4f2", + ], + "id": "dv-24497150208846dbbb94cf13157d76d1", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1684,21 +1675,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -1707,18 +1686,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -1727,17 +1706,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -1746,18 +1725,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -1766,119 +1745,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243501:T:C", - "display": "NC_000019.9:11243501:T:C" - } - ] - } + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueString": "T" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "NC_000019.9:11243327:C:G", + "display": "NC_000019.9:11243327:C:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 11243327 + } + } + }, + { + "code": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 11243501 - } + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-57370e44f9884d8cb43661abf73c23c3", + ], + "id": "dv-9ad6695f56dd4d82afb319c8331d3a6d", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1886,21 +1877,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -1909,18 +1888,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -1929,17 +1908,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -1948,18 +1927,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -1968,18 +1947,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "C" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "T" + }, + { + "code": { + "coding": [ + { "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242657:T:C", - "display": "NC_000019.9:11242657:T:C" + "code": "NC_000019.9:11210927:C:T", + "display": "NC_000019.9:11210927:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -1988,99 +1991,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 11210927 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 7.96318e-06 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11242657 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-7811771c3f3344dca8b4fcf0f9fd84b1", + ], + "id": "dv-46597e63d927405d8818e0867d0e521c", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2088,21 +2095,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -2111,18 +2106,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -2131,17 +2126,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -2150,18 +2145,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -2170,119 +2165,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "C" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243591:G:T", - "display": "NC_000019.9:11243591:G:T" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243259:C:T", + "display": "NC_000019.9:11243259:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueRange": { + "low": { + "value": 11243259 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243591 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-904b6ac36b25461ea7a2304093bc6fec", + ], + "id": "dv-40f05bda5c564d8bb5d775df91b83873", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2290,21 +2297,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -2313,18 +2308,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -2333,17 +2328,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -2352,18 +2347,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -2372,79 +2367,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242306:G:C", - "display": "NC_000019.9:11242306:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.9:11243734:C:T", + "display": "NC_000019.9:11243734:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -2453,15 +2411,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 11242306 + "value": 11243734 } } }, @@ -2469,38 +2427,71 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.818994, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-930a27aa386d4cb8bff1e437040afb45", + ], + "id": "dv-a4bc1ce389c943248c967f087971ba88", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2508,21 +2499,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -2531,18 +2510,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -2551,17 +2530,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -2570,18 +2549,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -2590,18 +2569,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "A" + }, + { + "code": { + "coding": [ + { "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242764:A:G", - "display": "NC_000019.9:11242764:A:G" + "code": "NC_000019.9:11242043:G:A", + "display": "NC_000019.9:11242043:G:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -2610,99 +2613,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 11242043 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.243375 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11242764 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-9911e411d71f41789c58a251995db6ab", + ], + "id": "dv-ec3a667068394825be063d587250d6e2", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2710,21 +2717,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -2733,18 +2728,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -2753,17 +2748,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -2772,18 +2767,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -2792,119 +2787,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "G" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243208:C:AG", - "display": "NC_000019.9:11243208:C:AG" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11242495:G:A", + "display": "NC_000019.9:11242495:G:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "AC" + "valueRange": { + "low": { + "value": 11242495 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "AAG" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11243207 - } - } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-9ad6695f56dd4d82afb319c8331d3a6d", + ], + "id": "dv-25751058304a4b40a5254642589509ae", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2912,21 +2919,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -2935,18 +2930,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -2955,17 +2950,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -2974,18 +2969,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -2994,119 +2989,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "G" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243327:C:G", - "display": "NC_000019.9:11243327:C:G" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243159:G:A", + "display": "NC_000019.9:11243159:G:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueRange": { + "low": { + "value": 11243159 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243327 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-a4bc1ce389c943248c967f087971ba88", + ], + "id": "dv-ae2c1cd27dd44fb79b1b949e56ae7833", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3114,21 +3121,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -3137,18 +3132,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -3157,17 +3152,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -3176,18 +3171,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -3196,141 +3191,141 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "G" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243734:C:T", - "display": "NC_000019.9:11243734:C:T" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243591:G:T", + "display": "NC_000019.9:11243591:G:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueRange": { + "low": { + "value": 11243591 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243734 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-ae2c1cd27dd44fb79b1b949e56ae7833", + ], + "id": "dv-7811771c3f3344dca8b4fcf0f9fd84b1", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, "subject": { "reference": "Patient/HG00403" }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -3339,18 +3334,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -3359,17 +3354,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -3378,18 +3373,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -3398,119 +3393,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "T" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243159:G:A", - "display": "NC_000019.9:11243159:G:A" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243367:T:C", + "display": "NC_000019.9:11243367:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueRange": { + "low": { + "value": 11243367 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243159 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-d5e6a6a584a44454901740ac1d9c4b1f", + ], + "id": "dv-3bd5a669b6b14313bb6585f4f0249b8e", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3518,21 +3525,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -3541,18 +3536,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -3561,17 +3556,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -3580,18 +3575,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -3600,119 +3595,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "T" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243223:CTACTA:CTA", - "display": "NC_000019.9:11243223:CTACTA:CTA" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243501:T:C", + "display": "NC_000019.9:11243501:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "TCTA" + "valueRange": { + "low": { + "value": 11243501 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243222 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-ec3a667068394825be063d587250d6e2", + ], + "id": "dv-5459aa2045a740c0af8c14cbc66cd4f2", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3720,21 +3727,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -3743,18 +3738,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -3763,17 +3758,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -3782,99 +3777,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242043:G:A", - "display": "NC_000019.9:11242043:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueString": "TCTA" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.9:11243223:CTACTA:CTA", + "display": "NC_000019.9:11243223:CTACTA:CTA", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -3883,15 +3841,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 11242043 + "value": 11243222 } } }, @@ -3899,22 +3857,64 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.243375, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] + ], + "id": "dv-d5e6a6a584a44454901740ac1d9c4b1f", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_variants/3.json b/tests/expected_outputs/find_subject_variants/3.json index b030ddaff..930d8caa8 100644 --- a/tests/expected_outputs/find_subject_variants/3.json +++ b/tests/expected_outputs/find_subject_variants/3.json @@ -1,34 +1,25 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ - { - "name": "rangeItem", - "valueString": "NC_000019.10:11089431-11133820" - }, { "name": "presence", "valueBoolean": true }, + { + "name": "rangeItem", + "valueString": "NC_000019.10:11089431-11133820" + }, { "name": "variant", "resource": { - "resourceType": "Observation", - "id": "dv-0cbf052b7dc2453c83798496893eeb8a", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -36,21 +27,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -59,18 +38,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -79,17 +58,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -98,18 +77,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6705-3", - "display": "homozygous" + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -118,18 +97,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "A" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, + { + "code": { + "coding": [ + { "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243253:T:C", - "display": "NC_000019.9:11243253:T:C" + "code": "NC_000019.9:11233940:A:G", + "display": "NC_000019.9:11233940:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -138,99 +141,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 11233940 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.781146 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243253 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-24497150208846dbbb94cf13157d76d1", + ], + "id": "dv-3f58c03ccc244f01820bf9445e076d69", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -238,21 +245,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -261,18 +256,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -281,17 +276,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -300,18 +295,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -320,119 +315,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "AC" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243331:C:A", - "display": "NC_000019.9:11243331:C:A" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "AAG" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243208:C:AG", + "display": "NC_000019.9:11243208:C:AG", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueRange": { + "low": { + "value": 11243207 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243331 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-25751058304a4b40a5254642589509ae", + ], + "id": "dv-9911e411d71f41789c58a251995db6ab", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -440,21 +447,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -463,18 +458,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -483,17 +478,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -502,18 +497,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -522,18 +517,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "C" + }, + { + "code": { + "coding": [ + { "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242495:G:A", - "display": "NC_000019.9:11242495:G:A" + "code": "NC_000019.9:11242306:G:C", + "display": "NC_000019.9:11242306:G:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -542,99 +561,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 11242306 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.818994 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11242495 - } - } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-3bd5a669b6b14313bb6585f4f0249b8e", + ], + "id": "dv-904b6ac36b25461ea7a2304093bc6fec", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -642,21 +665,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -665,18 +676,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -685,17 +696,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -704,18 +715,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6706-1", - "display": "heterozygous" + "code": "LA6705-3", + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -724,119 +735,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "T" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243367:T:C", - "display": "NC_000019.9:11243367:T:C" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11242657:T:C", + "display": "NC_000019.9:11242657:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueRange": { + "low": { + "value": 11242657 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243367 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-3f58c03ccc244f01820bf9445e076d69", + ], + "id": "dv-57370e44f9884d8cb43661abf73c23c3", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -844,21 +867,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -867,18 +878,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -887,17 +898,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -906,99 +917,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6705-3", - "display": "homozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11233940:A:G", - "display": "NC_000019.9:11233940:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "display": "homozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.9:11243253:T:C", + "display": "NC_000019.9:11243253:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -1007,15 +981,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 11233940 + "value": 11243253 } } }, @@ -1023,38 +997,71 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.781146, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-40f05bda5c564d8bb5d775df91b83873", + ], + "id": "dv-0cbf052b7dc2453c83798496893eeb8a", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1062,21 +1069,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -1085,18 +1080,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -1105,17 +1100,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -1124,18 +1119,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -1144,119 +1139,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243259:C:T", - "display": "NC_000019.9:11243259:C:T" - } - ] - } + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueString": "C" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "NC_000019.9:11242764:A:G", + "display": "NC_000019.9:11242764:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] - }, - "valueString": "T" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 11242764 + } + } + }, + { + "code": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 11243259 - } + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-46597e63d927405d8818e0867d0e521c", + ], + "id": "dv-930a27aa386d4cb8bff1e437040afb45", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1264,21 +1271,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -1287,18 +1282,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -1307,17 +1302,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -1326,99 +1321,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11210927:C:T", - "display": "NC_000019.9:11210927:C:T" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.9:11243444:A:G", + "display": "NC_000019.9:11243444:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -1427,15 +1385,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 11210927 + "value": 11243444 } } }, @@ -1443,38 +1401,71 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 7.96318e-06, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", + ], "id": "dv-47e65009ae414a218cf7efe34f83c3e0", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1482,21 +1473,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -1505,18 +1484,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -1525,17 +1504,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -1544,18 +1523,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -1564,119 +1543,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "C" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243444:A:G", - "display": "NC_000019.9:11243444:A:G" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243331:C:A", + "display": "NC_000019.9:11243331:C:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueRange": { + "low": { + "value": 11243331 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243444 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-5459aa2045a740c0af8c14cbc66cd4f2", + ], + "id": "dv-24497150208846dbbb94cf13157d76d1", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1684,21 +1675,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -1707,18 +1686,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -1727,17 +1706,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -1746,18 +1725,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -1766,119 +1745,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243501:T:C", - "display": "NC_000019.9:11243501:T:C" - } - ] - } + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } + "valueString": "G" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueString": "T" - }, - { - "code": { + "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "NC_000019.9:11243327:C:G", + "display": "NC_000019.9:11243327:C:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] - }, - "valueString": "C" + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueRange": { + "low": { + "value": 11243327 + } + } + }, + { + "code": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, - "valueRange": { - "low": { - "value": 11243501 - } + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-57370e44f9884d8cb43661abf73c23c3", + ], + "id": "dv-9ad6695f56dd4d82afb319c8331d3a6d", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -1886,21 +1877,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -1909,18 +1888,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -1929,17 +1908,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -1948,18 +1927,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -1968,18 +1947,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "C" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "T" + }, + { + "code": { + "coding": [ + { "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242657:T:C", - "display": "NC_000019.9:11242657:T:C" + "code": "NC_000019.9:11210927:C:T", + "display": "NC_000019.9:11210927:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -1988,99 +1991,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 11210927 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 7.96318e-06 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11242657 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-7811771c3f3344dca8b4fcf0f9fd84b1", + ], + "id": "dv-46597e63d927405d8818e0867d0e521c", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2088,21 +2095,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -2111,18 +2106,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -2131,17 +2126,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -2150,18 +2145,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -2170,119 +2165,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "C" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243591:G:T", - "display": "NC_000019.9:11243591:G:T" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243259:C:T", + "display": "NC_000019.9:11243259:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueRange": { + "low": { + "value": 11243259 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243591 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-904b6ac36b25461ea7a2304093bc6fec", + ], + "id": "dv-40f05bda5c564d8bb5d775df91b83873", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2290,21 +2297,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -2313,18 +2308,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -2333,17 +2328,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -2352,18 +2347,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -2372,79 +2367,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242306:G:C", - "display": "NC_000019.9:11242306:G:C" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" - } - ] - }, - "valueString": "G" + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.9:11243734:C:T", + "display": "NC_000019.9:11243734:C:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -2453,15 +2411,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 11242306 + "value": 11243734 } } }, @@ -2469,38 +2427,71 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.818994, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-930a27aa386d4cb8bff1e437040afb45", + ], + "id": "dv-a4bc1ce389c943248c967f087971ba88", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2508,21 +2499,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -2531,18 +2510,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -2551,17 +2530,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -2570,18 +2549,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -2590,18 +2569,42 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "G" + }, + { + "code": { + "coding": [ + { + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" + } + ] + }, + "valueString": "A" + }, + { + "code": { + "coding": [ + { "code": "81252-9", - "display": "Discrete genetic variant" + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242764:A:G", - "display": "NC_000019.9:11242764:A:G" + "code": "NC_000019.9:11242043:G:A", + "display": "NC_000019.9:11242043:G:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -2610,99 +2613,103 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueRange": { + "low": { + "value": 11242043 + } } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "92821-8", + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "value": 0.243375 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11242764 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-9911e411d71f41789c58a251995db6ab", + ], + "id": "dv-ec3a667068394825be063d587250d6e2", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2710,21 +2717,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -2733,18 +2728,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -2753,17 +2748,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -2772,18 +2767,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA6705-3", - "display": "homozygous" + "code": "LA6706-1", + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -2792,119 +2787,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "G" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243208:C:AG", - "display": "NC_000019.9:11243208:C:AG" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11242495:G:A", + "display": "NC_000019.9:11242495:G:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "AC" + "valueRange": { + "low": { + "value": 11242495 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "AAG" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" - } - ] - }, - "valueRange": { - "low": { - "value": 11243207 - } - } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-9ad6695f56dd4d82afb319c8331d3a6d", + ], + "id": "dv-25751058304a4b40a5254642589509ae", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -2912,21 +2919,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -2935,18 +2930,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -2955,17 +2950,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -2974,18 +2969,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -2994,119 +2989,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "G" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243327:C:G", - "display": "NC_000019.9:11243327:C:G" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "A" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243159:G:A", + "display": "NC_000019.9:11243159:G:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueRange": { + "low": { + "value": 11243159 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243327 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-a4bc1ce389c943248c967f087971ba88", + ], + "id": "dv-ae2c1cd27dd44fb79b1b949e56ae7833", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3114,21 +3121,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -3137,18 +3132,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -3157,17 +3152,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -3176,18 +3171,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -3196,141 +3191,141 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "G" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243734:C:T", - "display": "NC_000019.9:11243734:C:T" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243591:G:T", + "display": "NC_000019.9:11243591:G:T", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "C" + "valueRange": { + "low": { + "value": 11243591 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243734 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-ae2c1cd27dd44fb79b1b949e56ae7833", + ], + "id": "dv-7811771c3f3344dca8b4fcf0f9fd84b1", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, "subject": { "reference": "Patient/HG00403" }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -3339,18 +3334,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -3359,17 +3354,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -3378,18 +3373,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -3398,119 +3393,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "T" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243159:G:A", - "display": "NC_000019.9:11243159:G:A" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243367:T:C", + "display": "NC_000019.9:11243367:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueRange": { + "low": { + "value": 11243367 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243159 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-d5e6a6a584a44454901740ac1d9c4b1f", + ], + "id": "dv-3bd5a669b6b14313bb6585f4f0249b8e", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3518,21 +3525,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -3541,18 +3536,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -3561,17 +3556,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -3580,18 +3575,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -3600,119 +3595,131 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" + "code": "69547-8", + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueCodeableConcept": { + "valueString": "T" + }, + { + "code": { "coding": [ { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11243223:CTACTA:CTA", - "display": "NC_000019.9:11243223:CTACTA:CTA" + "code": "69551-0", + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] - } + }, + "valueString": "C" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" + "valueCodeableConcept": { + "coding": [ + { + "code": "NC_000019.9:11243501:T:C", + "display": "NC_000019.9:11243501:T:C", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" + } + ] } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "code": "81254-5", + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, - "valueString": "TCTA" + "valueRange": { + "low": { + "value": 11243501 + } + } }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, - "valueString": "T" + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "92822-6", - "display": "Genomic coord system" + "display": "Genomic coord system", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA30100-4", - "display": "0-based interval counting" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81254-5", - "display": "Variant exact start-end" + "display": "0-based interval counting", + "system": "http://loinc.org" } ] - }, - "valueRange": { - "low": { - "value": 11243222 - } } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-ec3a667068394825be063d587250d6e2", + ], + "id": "dv-5459aa2045a740c0af8c14cbc66cd4f2", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -3720,21 +3727,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -3743,18 +3738,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -3763,17 +3758,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000019.9" + "code": "NC_000019.9", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -3782,99 +3777,62 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000019.9:11242043:G:A", - "display": "NC_000019.9:11242043:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "G" + "valueString": "TCTA" }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, - "valueString": "A" + "valueString": "T" }, { "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000019.9:11243223:CTACTA:CTA", + "display": "NC_000019.9:11243223:CTACTA:CTA", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -3883,15 +3841,15 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, "valueRange": { "low": { - "value": 11242043 + "value": 11243222 } } }, @@ -3899,22 +3857,64 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92821-8", - "display": "Population allele frequency" + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.243375, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] + ], + "id": "dv-d5e6a6a584a44454901740ac1d9c4b1f", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_variants/4.json b/tests/expected_outputs/find_subject_variants/4.json index 34c7330d1..8b07598f3 100644 --- a/tests/expected_outputs/find_subject_variants/4.json +++ b/tests/expected_outputs/find_subject_variants/4.json @@ -1,18 +1,18 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ - { - "name": "rangeItem", - "valueString": "NC_000019.9:11221327-11221447" - }, { "name": "presence", "valueBoolean": false + }, + { + "name": "rangeItem", + "valueString": "NC_000019.9:11221327-11221447" } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_variants/5.json b/tests/expected_outputs/find_subject_variants/5.json index 71c784f5a..87beef16b 100644 --- a/tests/expected_outputs/find_subject_variants/5.json +++ b/tests/expected_outputs/find_subject_variants/5.json @@ -1,34 +1,25 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ - { - "name": "rangeItem", - "valueString": "NC_000001.10:69501-69520" - }, { "name": "presence", "valueBoolean": true }, + { + "name": "rangeItem", + "valueString": "NC_000001.10:69501-69520" + }, { "name": "variant", "resource": { - "resourceType": "Observation", - "id": "dv-a19d3986a732490eb7a56a9dacf55175", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -36,21 +27,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -59,18 +38,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -79,17 +58,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000001.10" + "code": "NC_000001.10", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -98,18 +77,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6705-3", - "display": "homozygous" + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -118,46 +97,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000001.10:69510:A:G", - "display": "NC_000001.10:69510:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -167,9 +109,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, @@ -179,18 +121,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000001.10:69510:A:G", + "display": "NC_000001.10:69510:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -199,9 +141,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, @@ -215,19 +157,76 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" + } + ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } + }, + { + "code": { + "coding": [ + { "code": "92821-8", - "display": "Population allele frequency" + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.949691, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "value": 0.949691 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] + ], + "id": "dv-a19d3986a732490eb7a56a9dacf55175", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } ] @@ -235,31 +234,23 @@ { "name": "variants", "part": [ - { - "name": "rangeItem", - "valueString": "NC_000001.10:69501-69521" - }, { "name": "presence", "valueBoolean": true }, + { + "name": "rangeItem", + "valueString": "NC_000001.10:69501-69521" + }, { "name": "variant", "resource": { - "resourceType": "Observation", - "id": "dv-a19d3986a732490eb7a56a9dacf55175", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -267,21 +258,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/HG00403" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -290,18 +269,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -310,17 +289,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000001.10" + "code": "NC_000001.10", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -329,18 +308,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6705-3", - "display": "homozygous" + "display": "homozygous", + "system": "http://loinc.org" } ] } @@ -349,46 +328,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000001.10:69510:A:G", - "display": "NC_000001.10:69510:A:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 1.0, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -398,9 +340,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, @@ -410,18 +352,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000001.10:69510:A:G", + "display": "NC_000001.10:69510:A:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -430,9 +372,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, @@ -446,22 +388,80 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" + } + ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 1.0 + } + }, + { + "code": { + "coding": [ + { "code": "92821-8", - "display": "Population allele frequency" + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.949691, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "value": 0.949691 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] + ], + "id": "dv-a19d3986a732490eb7a56a9dacf55175", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + ] + }, + "resourceType": "Observation", + "status": "final", + "subject": { + "reference": "Patient/HG00403" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } } } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_subject_variants/6.json b/tests/expected_outputs/find_subject_variants/6.json index f4fd84f7c..8c3584a8d 100644 --- a/tests/expected_outputs/find_subject_variants/6.json +++ b/tests/expected_outputs/find_subject_variants/6.json @@ -1,34 +1,25 @@ { - "resourceType": "Parameters", "parameter": [ { "name": "variants", "part": [ - { - "name": "rangeItem", - "valueString": "NC_000001.11:2629432-2629470" - }, { "name": "presence", "valueBoolean": true }, { - "name": "variant", + "name": "rangeItem", + "valueString": "NC_000001.11:2629432-2629470" + }, + { + "name": "sequencePhaseRelationship", "resource": { - "resourceType": "Observation", - "id": "dv-0ff7e9652c4a466ea69b705261adc0f8", - "meta": { - "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" - ] - }, - "status": "final", "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -36,21 +27,61 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "69548-6", - "display": "Genetic variant assessment" + "code": "82120-7", + "display": "Allelic phase", + "system": "http://loinc.org" } ] }, + "derivedFrom": [ + { + "reference": "Observation/dv-0ff7e9652c4a466ea69b705261adc0f8" + }, + { + "reference": "Observation/dv-2d4c28cebcc840dd98e7a62890cde178" + } + ], + "id": "sid-666243c731064e36481992ea", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship" + ] + }, + "resourceType": "Observation", + "status": "final", "subject": { "reference": "Patient/NB6TK329" }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "code": "Cis", + "display": "Cis", + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/sequence-phase-relationship-cs" + } + ] + } + } + }, + { + "name": "variant", + "resource": { + "category": [ + { + "coding": [ + { + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" + } + ] + } + ], + "code": { + "coding": [ + { + "code": "69548-6", + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -59,18 +90,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -79,17 +110,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000001.11" + "code": "NC_000001.11", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -98,66 +129,29 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000001.11:2629442:G:A", - "display": "NC_000001.11:2629442:G:A" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" + "display": "heterozygous", + "system": "http://loinc.org" } ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" } }, { "code": { "coding": [ { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -167,9 +161,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, @@ -179,18 +173,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000001.11:2629442:G:A", + "display": "NC_000001.11:2629442:G:A", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -199,9 +193,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, @@ -215,38 +209,87 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" + } + ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { + "coding": [ + { "code": "92821-8", - "display": "Population allele frequency" + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.58297, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "value": 0.58297 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "variant", - "resource": { - "resourceType": "Observation", - "id": "dv-2d4c28cebcc840dd98e7a62890cde178", + ], + "id": "dv-0ff7e9652c4a466ea69b705261adc0f8", "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", + "subject": { + "reference": "Patient/NB6TK329" + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" + } + ] + } + } + }, + { + "name": "variant", + "resource": { "category": [ { "coding": [ { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" + "code": "laboratory", + "system": "http://terminology.hl7.org/CodeSystem/observation-category" } ] } @@ -254,21 +297,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69548-6", - "display": "Genetic variant assessment" - } - ] - }, - "subject": { - "reference": "Patient/NB6TK329" - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "http://loinc.org", - "code": "LA9633-4", - "display": "present" + "display": "Genetic variant assessment", + "system": "http://loinc.org" } ] }, @@ -277,18 +308,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48002-0", - "display": "Genomic Source Class" + "display": "Genomic Source Class", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6683-2", - "display": "germline" + "display": "germline", + "system": "http://loinc.org" } ] } @@ -297,17 +328,17 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "48013-7", - "display": "Genomic reference sequence ID" + "display": "Genomic reference sequence ID", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://www.ncbi.nlm.nih.gov/nuccore", - "code": "NC_000001.11" + "code": "NC_000001.11", + "system": "http://www.ncbi.nlm.nih.gov/nuccore" } ] } @@ -316,18 +347,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "53034-5", - "display": "Allelic state" + "display": "Allelic state", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", "code": "LA6706-1", - "display": "heterozygous" + "display": "heterozygous", + "system": "http://loinc.org" } ] } @@ -336,46 +367,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "81252-9", - "display": "Discrete genetic variant" - } - ] - }, - "valueCodeableConcept": { - "coding": [ - { - "system": "https://api.ncbi.nlm.nih.gov/variation/v0/", - "code": "NC_000001.11:2629463:T:G", - "display": "NC_000001.11:2629463:T:G" - } - ] - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "81258-6", - "display": "Sample VAF" - } - ] - }, - "valueQuantity": { - "value": 0.5, - "unit": "relative frequency of a particular allele in the specimen", - "system": "http://unitsofmeasure.org", - "code": "1" - } - }, - { - "code": { - "coding": [ - { - "system": "http://loinc.org", "code": "69547-8", - "display": "Genomic Ref allele [ID]" + "display": "Genomic Ref allele [ID]", + "system": "http://loinc.org" } ] }, @@ -385,9 +379,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "69551-0", - "display": "Genomic Alt allele [ID]" + "display": "Genomic Alt allele [ID]", + "system": "http://loinc.org" } ] }, @@ -397,18 +391,18 @@ "code": { "coding": [ { - "system": "http://loinc.org", - "code": "92822-6", - "display": "Genomic coord system" + "code": "81252-9", + "display": "Discrete genetic variant", + "system": "http://loinc.org" } ] }, "valueCodeableConcept": { "coding": [ { - "system": "http://loinc.org", - "code": "LA30100-4", - "display": "0-based interval counting" + "code": "NC_000001.11:2629463:T:G", + "display": "NC_000001.11:2629463:T:G", + "system": "https://api.ncbi.nlm.nih.gov/variation/v0/" } ] } @@ -417,9 +411,9 @@ "code": { "coding": [ { - "system": "http://loinc.org", "code": "81254-5", - "display": "Variant exact start-end" + "display": "Variant exact start-end", + "system": "http://loinc.org" } ] }, @@ -433,74 +427,80 @@ "code": { "coding": [ { - "system": "http://loinc.org", + "code": "81258-6", + "display": "Sample VAF", + "system": "http://loinc.org" + } + ] + }, + "valueQuantity": { + "code": "1", + "system": "http://unitsofmeasure.org", + "unit": "relative frequency of a particular allele in the specimen", + "value": 0.5 + } + }, + { + "code": { + "coding": [ + { "code": "92821-8", - "display": "Population allele frequency" + "display": "Population allele frequency", + "system": "http://loinc.org" } ] }, "valueQuantity": { - "value": 0.600482, + "code": "1", "system": "http://unitsofmeasure.org", - "code": "1" + "value": 0.600482 + } + }, + { + "code": { + "coding": [ + { + "code": "92822-6", + "display": "Genomic coord system", + "system": "http://loinc.org" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "code": "LA30100-4", + "display": "0-based interval counting", + "system": "http://loinc.org" + } + ] } } - ] - } - }, - { - "name": "sequencePhaseRelationship", - "resource": { - "resourceType": "Observation", - "id": "sid-666243c731064e36481992ea", + ], + "id": "dv-2d4c28cebcc840dd98e7a62890cde178", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ] }, + "resourceType": "Observation", "status": "final", - "category": [ - { - "coding": [ - { - "system": "http://terminology.hl7.org/CodeSystem/observation-category", - "code": "laboratory" - } - ] - } - ], - "code": { - "coding": [ - { - "system": "http://loinc.org", - "code": "82120-7", - "display": "Allelic phase" - } - ] - }, "subject": { "reference": "Patient/NB6TK329" }, "valueCodeableConcept": { "coding": [ { - "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/sequence-phase-relationship-cs", - "code": "Cis", - "display": "Cis" + "code": "LA9633-4", + "display": "present", + "system": "http://loinc.org" } ] - }, - "derivedFrom": [ - { - "reference": "Observation/dv-0ff7e9652c4a466ea69b705261adc0f8" - }, - { - "reference": "Observation/dv-2d4c28cebcc840dd98e7a62890cde178" - } - ] + } } } ] } - ] + ], + "resourceType": "Parameters" } \ No newline at end of file diff --git a/tests/expected_outputs/find_the_gene/1.json b/tests/expected_outputs/find_the_gene/1.json index 0976f77df..2ebb3dccd 100644 --- a/tests/expected_outputs/find_the_gene/1.json +++ b/tests/expected_outputs/find_the_gene/1.json @@ -1,16 +1,16 @@ [ { - "geneId": "HGNC:7436", - "geneSymbol": "MTHFR", - "geneLink": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:7436", + "MANE": [ + "NM_005957.5" + ], "build37Coordinates": "NC_000001.10:11845779-11866021", "build38Coordinates": "NC_000001.11:11785722-11806103", + "geneId": "HGNC:7436", + "geneLink": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:7436", + "geneSymbol": "MTHFR", "transcripts": [ "NM_001330358.2", "NM_005957.5" - ], - "MANE": [ - "NM_005957.5" ] } ] \ No newline at end of file diff --git a/tests/expected_outputs/get_feature_coordinates/1.json b/tests/expected_outputs/get_feature_coordinates/1.json index 955cc766b..40d08ca7a 100644 --- a/tests/expected_outputs/get_feature_coordinates/1.json +++ b/tests/expected_outputs/get_feature_coordinates/1.json @@ -1,6 +1,6 @@ { - "chromosome": "chr1", - "chromosomeLink": "https://medlineplus.gov/genetics/chromosome/1/", "build37RefSeq": "NC_000001.10", - "build38RefSeq": "NC_000001.11" + "build38RefSeq": "NC_000001.11", + "chromosome": "chr1", + "chromosomeLink": "https://medlineplus.gov/genetics/chromosome/1/" } \ No newline at end of file diff --git a/tests/expected_outputs/get_feature_coordinates/2.json b/tests/expected_outputs/get_feature_coordinates/2.json index 42828cb10..df30ecb21 100644 --- a/tests/expected_outputs/get_feature_coordinates/2.json +++ b/tests/expected_outputs/get_feature_coordinates/2.json @@ -1,6 +1,6 @@ { - "chromosome": "chrM", - "chromosomeLink": "https://medlineplus.gov/genetics/chromosome/mitochondrial-dna/", "build37RefSeq": "NC_012920.1", - "build38RefSeq": "NC_012920.1" + "build38RefSeq": "NC_012920.1", + "chromosome": "chrM", + "chromosomeLink": "https://medlineplus.gov/genetics/chromosome/mitochondrial-dna/" } \ No newline at end of file diff --git a/tests/expected_outputs/get_feature_coordinates/3.json b/tests/expected_outputs/get_feature_coordinates/3.json index 0ba83c423..5e2ea47fc 100644 --- a/tests/expected_outputs/get_feature_coordinates/3.json +++ b/tests/expected_outputs/get_feature_coordinates/3.json @@ -1,6 +1,6 @@ { - "chromosome": "chrY", - "chromosomeLink": "https://medlineplus.gov/genetics/chromosome/y/", "build37RefSeq": "NC_000024.9", - "build38RefSeq": "NC_000024.10" + "build38RefSeq": "NC_000024.10", + "chromosome": "chrY", + "chromosomeLink": "https://medlineplus.gov/genetics/chromosome/y/" } \ No newline at end of file diff --git a/tests/expected_outputs/get_feature_coordinates/4.json b/tests/expected_outputs/get_feature_coordinates/4.json index 927d60f08..5e177c297 100644 --- a/tests/expected_outputs/get_feature_coordinates/4.json +++ b/tests/expected_outputs/get_feature_coordinates/4.json @@ -1,15 +1,15 @@ [ { - "geneId": "HGNC:5", - "geneSymbol": "A1BG", - "geneLink": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:5", + "MANE": [ + "NM_130786.4" + ], "build37Coordinates": "NC_000019.9:58856548-58864858", "build38Coordinates": "NC_000019.10:58345182-58353492", + "geneId": "HGNC:5", + "geneLink": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:5", + "geneSymbol": "A1BG", "transcripts": [ "NM_130786.4" - ], - "MANE": [ - "NM_130786.4" ] } ] \ No newline at end of file diff --git a/tests/expected_outputs/get_feature_coordinates/5.json b/tests/expected_outputs/get_feature_coordinates/5.json index 3193469dc..0cb8d9c77 100644 --- a/tests/expected_outputs/get_feature_coordinates/5.json +++ b/tests/expected_outputs/get_feature_coordinates/5.json @@ -1,198 +1,198 @@ [ { - "transcript": "NM_000014.6", - "transcriptLink": "https://www.ncbi.nlm.nih.gov/nuccore/NM_000014.6", - "geneSymbol": "A2M", - "build37Coordinates": "NC_000012.11:9220303-9268515", - "build38Coordinates": "NC_000012.12:9067707-9115919", "MANE": true, - "build38CDSStart": 9067822, - "build38CDSEnd": 9115849, - "build38Strand": "-", - 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"exonNumber": 1 } - ] + ], + "geneSymbol": "A2M", + "transcript": "NM_000014.6", + "transcriptLink": "https://www.ncbi.nlm.nih.gov/nuccore/NM_000014.6" } ] \ No newline at end of file diff --git a/tests/expected_outputs/sort_json_data/nested.json b/tests/expected_outputs/sort_json_data/nested.json new file mode 100644 index 000000000..54fe87514 --- /dev/null +++ b/tests/expected_outputs/sort_json_data/nested.json @@ -0,0 +1,35 @@ +{ + "fruits": [ + { + "examples": [ + { + "common-name": "strawberry", + "name": "achenes" + }, + { + "members": [ + { + "common-name": "blackberry" + }, + { + "common-name": "raspberry" + } + ], + "name": "drupelets" + } + ], + "type": "aggregate" + }, + { + "examples": [ + { + "name": "apple" + }, + { + "name": "cherries" + } + ], + "type": "simple-fruits" + } + ] +} diff --git a/tests/expected_outputs/sort_json_data/simple.json b/tests/expected_outputs/sort_json_data/simple.json new file mode 100644 index 000000000..2e9a2e8db --- /dev/null +++ b/tests/expected_outputs/sort_json_data/simple.json @@ -0,0 +1,5 @@ +{ + "example": "apple", + "seeds?": "yes", + "type": "simple-fruit" +} diff --git a/tests/integration_tests/test_sort_json_data.py b/tests/integration_tests/test_sort_json_data.py new file mode 100644 index 000000000..9fcd3f1fb --- /dev/null +++ b/tests/integration_tests/test_sort_json_data.py @@ -0,0 +1,65 @@ +import json + +import tests.utilities as tu + +""" +Test JSON Sorting +------------------------------------- +""" +simple = { + "type": "simple-fruit", + "example": "apple", + "seeds?": "yes" +} + +simple_nested = { + "fruits": [ + { + "type": "simple-fruits", + "examples": [ + { + "name": "apple" + }, + { + "name": "cherries" + } + ] + }, + { + "type": "aggregate", + "examples": [ + { + "name": "drupelets", + "members": [ + { + "common-name": "raspberry" + }, + { + "common-name": "blackberry" + } + ] + }, + { + "name": "achenes", + "common-name": "strawberry" + } + ] + } + ] +} + + +def test_json_sorting_simple(): + sorted_actual = tu.sort_json_data(simple) + expected_loc = f'{tu.SORT_JSON_DATA_OUTPUT_DIR}simple.json' + with open(expected_loc) as expected_file: + expected_json = json.load(expected_file) + assert json.dumps(sorted_actual) == json.dumps(expected_json) + + +def test_json_sorting_nested(): + sorted_actual = tu.sort_json_data(simple_nested) + expected_loc = f'{tu.SORT_JSON_DATA_OUTPUT_DIR}nested.json' + with open(expected_loc) as expected_file: + expected_json = json.load(expected_file) + assert json.dumps(sorted_actual) == json.dumps(expected_json) diff --git a/tests/utilities.py b/tests/utilities.py index 95b036e58..2cff8a27e 100644 --- a/tests/utilities.py +++ b/tests/utilities.py @@ -63,6 +63,8 @@ NORMALIZE_HLA_URL = "/utilities/normalize-hla" NORMALIZE_HLA_OUTPUT_DIR = "tests/expected_outputs/normalize_hla/" +SORT_JSON_DATA_OUTPUT_DIR = "tests/expected_outputs/sort_json_data/" + def find_subject_variants_query(query): return f"{FIND_SUBJECT_VARIANTS_URL}?{query}" @@ -144,14 +146,29 @@ def normalize_hla_utility_query(query): return f"{NORMALIZE_HLA_URL}?{query}" +def sort_json_data(data): + """ + Recursively sorts the keys of a JSON object or the elements of a JSON list. + """ + if isinstance(data, dict): + return {k: sort_json_data(v) for k, v in sorted(data.items())} + elif isinstance(data, list): + return sorted((sort_json_data(v) for v in data), key=lambda x: json.dumps(x, sort_keys=True)) + + return data + + def compare_actual_and_expected_output(filename, actual_json): with open(filename) as expected_output_file: expected_json = json.load(expected_output_file) - diff = DeepDiff(actual_json, expected_json, ignore_order=True, report_repetition=True) + sorted_expected = sort_json_data(expected_json) + sorted_actual = sort_json_data(actual_json) + # TODO: It should suffice to just compare the sorted JSON strings, but this is more flexible + diff = DeepDiff(sorted_actual, sorted_expected, ignore_order=False, report_repetition=True) if diff != {}: if 'OVERWRITE_TEST_EXPECTED_DATA' in os.environ: with open(filename, 'w') as expected_output_file: - json.dump(actual_json, expected_output_file, indent=4) + json.dump(sorted_actual, expected_output_file, indent=4) else: - assert diff == {} + assert json.dumps(sorted_expected) == json.dumps(sorted_expected)