{
  "description": "Guidelines for reporting of clinical genomics results using HL7 FHIR",
  "_filename": "ImplementationGuide-hl7.fhir.uv.genomics-reporting.json",
  "package_name": "hl7.fhir.uv.genomics-reporting",
  "definition": {
    "page": {
      "page": [ {
        "page": [ {
          "title": "Genomics Background",
          "nameUrl": "background.html",
          "generation": "html"
        }, {
          "title": "General Genomic Reporting",
          "nameUrl": "general.html",
          "generation": "html"
        }, {
          "title": "Variant Reporting",
          "nameUrl": "sequencing.html",
          "generation": "html"
        }, {
          "title": "Glossary",
          "nameUrl": "Glossary.html",
          "generation": "html"
        }, {
          "title": "Pharmacogenomic Reporting",
          "nameUrl": "pharmacogenomics.html",
          "generation": "html"
        }, {
          "title": "Somatic Reporting",
          "nameUrl": "somatics.html",
          "generation": "html"
        }, {
          "title": "Histocompatibility and Immunogenetics Reporting",
          "nameUrl": "histocompatibility.html",
          "generation": "html"
        }, {
          "title": "Conversion from STU3",
          "nameUrl": "conversion.html",
          "generation": "html"
        }, {
          "title": "Appendix A: Relation to v2 reporting",
          "nameUrl": "v2.html",
          "generation": "html"
        }, {
          "title": "Appendix B: Clinical Genomic Apps",
          "nameUrl": "cgapps.html",
          "generation": "html"
        }, {
          "title": "Appendix C: HL7 Domain Analysis Model",
          "nameUrl": "domain.html",
          "generation": "html"
        }, {
          "title": "Appendix D: External Coding Systems",
          "nameUrl": "codings.html",
          "generation": "html"
        } ],
        "title": "IG Home Page",
        "nameUrl": "index.html",
        "generation": "html"
      }, {
        "page": [ {
          "title": "Genomics Base",
          "nameUrl": "genomics-base.html",
          "generation": "generated"
        }, {
          "title": "Genomics Report",
          "nameUrl": "genomics-report.html",
          "generation": "generated"
        }, {
          "title": "Specimen",
          "nameUrl": "specimen.html",
          "generation": "generated"
        }, {
          "title": "Recommended Followup",
          "nameUrl": "task-rec-followup.html",
          "generation": "generated"
        }, {
          "title": "Request for Genomics Test",
          "nameUrl": "servicerequest.html",
          "generation": "generated"
        }, {
          "title": "Grouper",
          "nameUrl": "grouper.html",
          "generation": "generated"
        }, {
          "title": "Overall Interpretation",
          "nameUrl": "overall-interpretation.html",
          "generation": "generated"
        }, {
          "title": "Genomic Finding",
          "nameUrl": "finding.html",
          "generation": "generated"
        }, {
          "title": "Haplotype",
          "nameUrl": "haplotype.html",
          "generation": "generated"
        }, {
          "title": "Genotype",
          "nameUrl": "genotype.html",
          "generation": "generated"
        }, {
          "title": "Variant",
          "nameUrl": "variant.html",
          "generation": "generated"
        }, {
          "title": "Sequence Phase Relationship",
          "nameUrl": "sequence-phase-relationship.html",
          "generation": "generated"
        }, {
          "title": "Genomic Implication",
          "nameUrl": "implication.html",
          "generation": "generated"
        }, {
          "title": "Inherited Disease Pathogenicity",
          "nameUrl": "inherited-disease-pathogenicity.html",
          "generation": "generated"
        }, {
          "title": "Region Studied",
          "nameUrl": "region-studied.html",
          "generation": "generated"
        }, {
          "title": "Medication Implication",
          "nameUrl": "medication-implication.html",
          "generation": "generated"
        }, {
          "title": "Medication Metabolism Implication",
          "nameUrl": "medication-metabolism.html",
          "generation": "generated"
        }, {
          "title": "Medication Transporter Implication",
          "nameUrl": "medication-transporter.html",
          "generation": "generated"
        }, {
          "title": "Medication Efficacy Implication",
          "nameUrl": "medication-efficacy.html",
          "generation": "generated"
        }, {
          "title": "High Risk Allele",
          "nameUrl": "medication-high-risk.html",
          "generation": "generated"
        }, {
          "title": "Medication Usage Implication",
          "nameUrl": "task-med-chg.html",
          "generation": "generated"
        }, {
          "title": "Current Medication",
          "nameUrl": "medicationstatement.html",
          "generation": "generated"
        }, {
          "title": "Somatic Implication",
          "nameUrl": "somatic-implication.html",
          "generation": "generated"
        }, {
          "title": "Somatic Diagnostic Implication",
          "nameUrl": "somatic-diagnostic.html",
          "generation": "generated"
        }, {
          "title": "Somatic Prognostic Implication",
          "nameUrl": "somatic-prognostic.html",
          "generation": "generated"
        }, {
          "title": "Somatic Predictive Implication",
          "nameUrl": "somatic-predictive.html",
          "generation": "generated"
        }, {
          "title": "Related Artifact",
          "nameUrl": "extension-RelatedArtifact.html",
          "generation": "generated"
        }, {
          "title": "Recommended Action",
          "nameUrl": "extension-RecommendedAction.html",
          "generation": "generated"
        }, {
          "title": "Supporting Information",
          "nameUrl": "extension-SupportingInfo.html",
          "generation": "generated"
        }, {
          "title": "Example - Genomics Reporting",
          "nameUrl": "diagnosticreport-cgexample.html",
          "generation": "generated"
        }, {
          "title": "Example - Pharmacogenomics",
          "nameUrl": "diagnosticreport-pgxexample.html",
          "generation": "generated"
        }, {
          "title": "Example - Full Bundle HLA genotyping for HLA-A, HLA-B, and HLA-C, using GLStrings",
          "nameUrl": "CG-IG-HLA-FullBundle-01.html",
          "generation": "generated"
        }, {
          "title": "Example - CYP2C19 report from 1000 Genomes",
          "nameUrl": "report-CYP2C19.html",
          "generation": "generated"
        }, {
          "title": "Example - subset of CYP2C19 report from 1000 Genomes showing phase",
          "nameUrl": "sequence-phase-relation-CYP2C19.html",
          "generation": "generated"
        }, {
          "title": "Example - Multiple Oncology Variant Report Example",
          "nameUrl": "oncology-report-example.html",
          "generation": "generated"
        }, {
          "title": "Example - Melanoma implication",
          "nameUrl": "oncology-diagnostic.html",
          "generation": "generated"
        }, {
          "title": "Example - Full Bundle Oncology Example",
          "nameUrl": "oncologyexamples-r4.html",
          "generation": "generated"
        }, {
          "title": "Example - Complex Variant (HGVS)",
          "nameUrl": "compound-heterozygote.html",
          "generation": "generated"
        }, {
          "title": "Example - Complex Variant (unpacked)",
          "nameUrl": "complexVariant-nonHGVS.html",
          "generation": "generated"
        }, {
          "title": "Example - NGS",
          "nameUrl": "SNVexample.html",
          "generation": "generated"
        }, {
          "title": "Example - Variant with ACMG Screening",
          "nameUrl": "AnnotationExample.html",
          "generation": "generated"
        }, {
          "title": "Example - High Risk Allele (HLA-B*15:02)",
          "nameUrl": "HLAB1502-pgx-example.html",
          "generation": "generated"
        }, {
          "title": "Example - Inherited Disease Pathogenicity",
          "nameUrl": "obs-idh-ex.html",
          "generation": "generated"
        }, {
          "title": "Example - HLA genotyping for HLA-A, HLA-B, and HLA-C, using GLStrings",
          "nameUrl": "diagnosticreport-hla-glstring-r4.html",
          "generation": "generated"
        }, {
          "title": "Example - HLA genotyping for HLA-A, using GLStrings",
          "nameUrl": "genotype-hla-a-glstring-r4.html",
          "generation": "generated"
        }, {
          "title": "Example - Observation for a single HLA-A allele",
          "nameUrl": "haplotype-hla-a-1-r4.html",
          "generation": "generated"
        }, {
          "title": "Example - Buccal swab for HLA typing",
          "nameUrl": "specimen-hla-r4.html",
          "generation": "generated"
        }, {
          "title": "Example - Service request for high-resolution HLA-A genotyping",
          "nameUrl": "servicerequest-hla-a-r4.html",
          "generation": "generated"
        }, {
          "title": "TBD Code System",
          "nameUrl": "tbd-codes.html",
          "generation": "generated"
        }, {
          "title": "Sequence Phase Relationship",
          "nameUrl": "seq-phase-relationship.html",
          "generation": "generated"
        }, {
          "title": "HGVS Value Set",
          "nameUrl": "valueset-hgvs.html",
          "generation": "generated"
        }, {
          "title": "HGNC Value Set",
          "nameUrl": "valueset-hgnc.html",
          "generation": "generated"
        }, {
          "title": "TBD Value Set",
          "nameUrl": "valueset-tbd-codes.html",
          "generation": "generated"
        }, {
          "title": "DNA Change Type",
          "nameUrl": "valueset-dna-change-type.html",
          "generation": "generated"
        }, {
          "title": "Functional Annotations",
          "nameUrl": "valueset-functional-annotation.html",
          "generation": "generated"
        }, {
          "title": "Sequence Phase Relationship",
          "nameUrl": "valueset-seq-phase-relationship.html",
          "generation": "generated"
        }, {
          "title": "Variant Inheritance",
          "nameUrl": "valueset-variant-inheritance.html",
          "generation": "generated"
        }, {
          "title": "Concept mapping for DNA Change Type",
          "nameUrl": "dna-change-type.html",
          "generation": "generated"
        } ],
        "title": "Artifact List",
        "nameUrl": "artifacts.html",
        "generation": "html"
      }, {
        "title": "Query Examples",
        "nameUrl": "usecases.html",
        "generation": "html"
      }, {
        "title": "Useful Downloads",
        "nameUrl": "downloads.html",
        "generation": "html"
      } ],
      "title": "Table of Contents",
      "nameUrl": "toc.html",
      "generation": "html"
    },
    "grouping": [ {
      "id": "general",
      "name": "General Profiles",
      "description": "General constraints on FHIR resources to be adhered to as part of the CG implementation guide that apply regardless of what area(s) of genomics are of interest"
    }, {
      "id": "somatics",
      "name": "Somatics",
      "description": "Profiles related to the reporting of somatic genomic issues"
    }, {
      "id": "pharmacogenomics",
      "name": "Pharmacogenomics",
      "description": "Profiles for reports relating to genomic implication on medication use and effectiveness"
    }, {
      "id": "abstract",
      "name": "Abstract",
      "description": "Abstract profiles holding common properties, outlining similarities in implementable profiles"
    }, {
      "id": "extensions",
      "name": "Extensions",
      "description": "Extensions defined as part of the CG implementation guide"
    }, {
      "id": "examples",
      "name": "Examples",
      "description": "Examples showing the use of the CG profiles"
    }, {
      "id": "codesystems",
      "name": "Code Systems",
      "description": "Code Systems defined in this implementation guide"
    }, {
      "id": "valuesets",
      "name": "Value Sets",
      "description": "Value Sets defined in this implementation guide"
    }, {
      "id": "conceptmaps",
      "name": "Concept Maps",
      "description": "Concept Maps defined in this implementation guide"
    }, {
      "id": "diagnosticreport-profile-spreadsheet.xml",
      "name": "GenomicsReport"
    }, {
      "id": "medicationstatement-profile-spreadsheet.xml",
      "name": "Medication Statement"
    }, {
      "id": "observation-profile-spreadsheet.xml",
      "name": "Observations"
    }, {
      "id": "servicerequest-profile-spreadsheet.xml",
      "name": "Service Request"
    }, {
      "id": "specimen-profile-spreadsheet.xml",
      "name": "Specimen"
    }, {
      "id": "task-profile-spreadsheet.xml",
      "name": "Task profiles"
    } ],
    "resource": [ {
      "name": "Example - Genomics Reporting",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "Bundle"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "diagnosticreport-cgexample.html"
      } ],
      "reference": {
        "reference": "Bundle/diagnosticreport-cgexample"
      },
      "groupingId": "examples",
      "description": "Test instance showing data from the CG v2 spec",
      "exampleCanonical": "StructureDefinition/overall-interpretation"
    }, {
      "name": "Example - Pharmacogenomics",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "Bundle"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "diagnosticreport-pgxexample.html"
      } ],
      "reference": {
        "reference": "Bundle/diagnosticreport-pgxexample"
      },
      "groupingId": "examples",
      "description": "Pharmacogenomic Report Example instances",
      "exampleCanonical": "StructureDefinition/medication-efficacy"
    }, {
      "name": "Example - Full Bundle HLA genotyping for HLA-A, HLA-B, and HLA-C, using GLStrings",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "Bundle"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "CG-IG-HLA-FullBundle-01.html"
      } ],
      "reference": {
        "reference": "Bundle/CG-IG-HLA-FullBundle-01"
      },
      "groupingId": "examples",
      "description": "Full Bundle HLA Typing Example",
      "exampleCanonical": "StructureDefinition/genomics-report"
    }, {
      "name": "Example - CYP2C19 report from 1000 Genomes",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "DiagnosticReport"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "report-CYP2C19.html"
      } ],
      "reference": {
        "reference": "DiagnosticReport/report-CYP2C19"
      },
      "groupingId": "examples",
      "description": "CYP2C19 report from 1000 Genomes",
      "exampleCanonical": "StructureDefinition/region-studied"
    }, {
      "name": "Example - subset of CYP2C19 report from 1000 Genomes showing phase",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "DiagnosticReport"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "sequence-phase-relation-CYP2C19.html"
      } ],
      "reference": {
        "reference": "DiagnosticReport/sequence-phase-relation-CYP2C19"
      },
      "groupingId": "examples",
      "description": "Phase relation on CYP2C19 report",
      "exampleCanonical": "StructureDefinition/sequence-phase-relationship"
    }, {
      "name": "Example - Multiple Oncology Variant Report Example",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "Bundle"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "oncology-report-example.html"
      } ],
      "reference": {
        "reference": "Bundle/oncology-report-example"
      },
      "groupingId": "examples",
      "description": "Oncology Example Report with 12 reported variants",
      "exampleCanonical": "StructureDefinition/genomics-report"
    }, {
      "name": "Example - Melanoma implication",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "Bundle"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "oncology-diagnostic.html"
      } ],
      "reference": {
        "reference": "Bundle/oncology-diagnostic"
      },
      "groupingId": "examples",
      "description": "Small example report with 1 reported variant and somatic diagnostic implication",
      "exampleCanonical": "StructureDefinition/somatic-diagnostic"
    }, {
      "name": "Example - Full Bundle Oncology Example",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "Bundle"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "oncologyexamples-r4.html"
      } ],
      "reference": {
        "reference": "Bundle/oncologyexamples-r4"
      },
      "groupingId": "examples",
      "description": "Full Bundle Oncology Example",
      "exampleCanonical": "StructureDefinition/somatic-predictive"
    }, {
      "name": "Example - Complex Variant (HGVS)",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "Bundle"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "compound-heterozygote.html"
      } ],
      "reference": {
        "reference": "Bundle/compound-heterozygote"
      },
      "groupingId": "examples",
      "description": "Compound Heterozygote Variant Example",
      "exampleCanonical": "StructureDefinition/variant"
    }, {
      "name": "Example - Complex Variant (unpacked)",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "Bundle"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "complexVariant-nonHGVS.html"
      } ],
      "reference": {
        "reference": "Bundle/complexVariant-nonHGVS"
      },
      "groupingId": "examples",
      "description": "Compound Heterozygote Variant example, using position, reference, and alternate allele instead of HGVS.",
      "exampleCanonical": "StructureDefinition/variant"
    }, {
      "name": "Example - NGS",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "Observation"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "SNVexample.html"
      } ],
      "reference": {
        "reference": "Observation/SNVexample"
      },
      "groupingId": "examples",
      "description": "SNV example",
      "exampleCanonical": "StructureDefinition/variant"
    }, {
      "name": "Example - Variant with ACMG Screening",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "DiagnosticReport"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "AnnotationExample.html"
      } ],
      "reference": {
        "reference": "DiagnosticReport/AnnotationExample"
      },
      "groupingId": "examples",
      "description": "ACMG annotated variant",
      "exampleCanonical": "StructureDefinition/genomics-report"
    }, {
      "name": "Example - High Risk Allele (HLA-B*15:02)",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "Bundle"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "HLAB1502-pgx-example.html"
      } ],
      "reference": {
        "reference": "Bundle/HLAB1502-pgx-example"
      },
      "groupingId": "examples",
      "description": "High Risk Allele (HLA-B*15:02)",
      "exampleCanonical": "StructureDefinition/medication-high-risk"
    }, {
      "name": "Example - Inherited Disease Pathogenicity",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "Observation"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-idh-ex.html"
      } ],
      "reference": {
        "reference": "Observation/obs-idh-ex"
      },
      "groupingId": "examples",
      "description": "Inherited Disease Pathogenicity",
      "exampleCanonical": "StructureDefinition/inherited-disease-pathogenicity"
    }, {
      "name": "Example - HLA genotyping for HLA-A, HLA-B, and HLA-C, using GLStrings",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "DiagnosticReport"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "diagnosticreport-hla-glstring-r4.html"
      } ],
      "reference": {
        "reference": "DiagnosticReport/diagnosticreport-hla-glstring-r4"
      },
      "groupingId": "examples",
      "description": "DiagnosticReport HLA Typing Example",
      "exampleCanonical": "StructureDefinition/genomics-report"
    }, {
      "name": "Example - HLA genotyping for HLA-A, using GLStrings",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "Observation"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "genotype-hla-a-glstring-r4.html"
      } ],
      "reference": {
        "reference": "Observation/genotype-hla-a-glstring-r4"
      },
      "groupingId": "examples",
      "description": "HLA-A genoyping Example: HLA-A*03:01:01:01+HLA-A*30:01:01",
      "exampleCanonical": "StructureDefinition/genotype"
    }, {
      "name": "Example - Observation for a single HLA-A allele",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "Observation"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "haplotype-hla-a-1-r4.html"
      } ],
      "reference": {
        "reference": "Observation/haplotype-hla-a-1-r4"
      },
      "groupingId": "examples",
      "description": "HLA-A allele observaation: HLA-A*03:01:01:01",
      "exampleCanonical": "StructureDefinition/haplotype"
    }, {
      "name": "Example - Buccal swab for HLA typing",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "Specimen"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "specimen-hla-r4.html"
      } ],
      "reference": {
        "reference": "Specimen/specimen-hla-r4"
      },
      "groupingId": "examples",
      "description": "Specimen example: Buccal swab for HLA typing",
      "exampleCanonical": "StructureDefinition/specimen"
    }, {
      "name": "Example - Service request for high-resolution HLA-A genotyping",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "ServiceRequest"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "servicerequest-hla-a-r4.html"
      } ],
      "reference": {
        "reference": "ServiceRequest/servicerequest-hla-a-r4"
      },
      "groupingId": "examples",
      "description": "ServiceRequest example: High-resolution HLA-A genotyping",
      "exampleCanonical": "StructureDefinition/servicerequest"
    }, {
      "name": "TBD Code System",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "CodeSystem"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "tbd-codes.html"
      } ],
      "reference": {
        "reference": "CodeSystem/tbd-codes"
      },
      "groupingId": "codesystems",
      "description": "Code System for codes yet to be defined in LOINC"
    }, {
      "name": "Sequence Phase Relationship",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "CodeSystem"
      }, {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "seq-phase-relationship.html"
      } ],
      "reference": {
        "reference": "CodeSystem/seq-phase-relationship"
      },
      "groupingId": "codesystems",
      "description": "Code System for specific types of relationships"
    }, {
      "name": "HGVS Value Set",
      "extension": [ {
        "url": "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
        "valueString": "ValueSet"
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