{
  "description": "Guidelines for reporting of clinical genomics results using HL7 FHIR",
  "_filename": "ImplementationGuide-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": "Cytogenomic Reporting",
          "nameUrl": "cytogenomics.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: Querying Genomics Information",
          "nameUrl": "domain.html",
          "generation": "html"
        } ],
        "title": "IG Home Page",
        "nameUrl": "index.html",
        "generation": "html"
      }, {
        "page": [ {
          "title": "Genetic Observation Common Properties",
          "nameUrl": "obs-base.html",
          "generation": "generated"
        }, {
          "title": "Genomics Report",
          "nameUrl": "diagnosticreport.html",
          "generation": "generated"
        }, {
          "title": "Specimen",
          "nameUrl": "specimen.html",
          "generation": "generated"
        }, {
          "title": "Recomended Followup",
          "nameUrl": "task-rec-followup.html",
          "generation": "generated"
        }, {
          "title": "Request for Genetics Test",
          "nameUrl": "servicerequest.html",
          "generation": "generated"
        }, {
          "title": "Genomics Panel",
          "nameUrl": "obs-gen-panel.html",
          "generation": "generated"
        }, {
          "title": "Genomic analysis overall interpretation",
          "nameUrl": "obs-overall.html",
          "generation": "generated"
        }, {
          "title": "Deletion-duplication overall interpretation",
          "nameUrl": "obs-deletion-dup.html",
          "generation": "generated"
        }, {
          "title": "Computable Genetic Finding",
          "nameUrl": "obs-comp-gen-finding.html",
          "generation": "generated"
        }, {
          "title": "Haplotype",
          "nameUrl": "obs-haplotype.html",
          "generation": "generated"
        }, {
          "title": "Genotype",
          "nameUrl": "obs-genotype.html",
          "generation": "generated"
        }, {
          "title": "Cytogenetic Nomenclature",
          "nameUrl": "obs-cytogenetic-nomenclature.html",
          "generation": "generated"
        }, {
          "title": "Complex Variant",
          "nameUrl": "obs-complex-variant.html",
          "generation": "generated"
        }, {
          "title": "Described Variant",
          "nameUrl": "obs-described-variant.html",
          "generation": "generated"
        }, {
          "title": "Sequence Phase Relationship",
          "nameUrl": "obs-sequence-phase-reltn.html",
          "generation": "generated"
        }, {
          "title": "Genetic Impact",
          "nameUrl": "obs-impact.html",
          "generation": "generated"
        }, {
          "title": "Inherited Disease Pathogenicity",
          "nameUrl": "obs-inh-dis-path.html",
          "generation": "generated"
        }, {
          "title": "Region Studied",
          "nameUrl": "obs-region-studied.html",
          "generation": "generated"
        }, {
          "title": "Copy Number Change",
          "nameUrl": "obs-copy-num-chg.html",
          "generation": "generated"
        }, {
          "title": "Device Microarray Platform",
          "nameUrl": "device-micro-plat.html",
          "generation": "generated"
        }, {
          "title": "Device FISH Probe",
          "nameUrl": "device-fish-probe.html",
          "generation": "generated"
        }, {
          "title": "Medication Impact",
          "nameUrl": "obs-med-impact.html",
          "generation": "generated"
        }, {
          "title": "Medication Metabolism Impact",
          "nameUrl": "obs-metabolism.html",
          "generation": "generated"
        }, {
          "title": "Medication Transporter Impact",
          "nameUrl": "obs-transporter.html",
          "generation": "generated"
        }, {
          "title": "Medication Efficacy Impact",
          "nameUrl": "obs-efficacy.html",
          "generation": "generated"
        }, {
          "title": "High Risk Allele",
          "nameUrl": "obs-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 Impact",
          "nameUrl": "obs-som-impact.html",
          "generation": "generated"
        }, {
          "title": "Somatic Diagnostic Impact",
          "nameUrl": "obs-som-diagnostic.html",
          "generation": "generated"
        }, {
          "title": "Somatic Prognostic Impact",
          "nameUrl": "obs-som-prognostic.html",
          "generation": "generated"
        }, {
          "title": "Somatic Predictive Impact",
          "nameUrl": "obs-som-predictive.html",
          "generation": "generated"
        }, {
          "title": "Related Artifact",
          "nameUrl": "extension-dr-relatedArtifact.html",
          "generation": "generated"
        }, {
          "title": "Recommended Action - DiagnosticReport",
          "nameUrl": "extension-dr-recommendedAction.html",
          "generation": "generated"
        }, {
          "title": "Supporting Information",
          "nameUrl": "extension-dr-supportingInfo.html",
          "generation": "generated"
        }, {
          "title": "Focus",
          "nameUrl": "extension-obs-focus.html",
          "generation": "generated"
        }, {
          "title": "Recommended Action - Observation",
          "nameUrl": "extension-obs-recommendedAction.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 - 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": "obs-genotype-hla-a-glstring-r4.html",
          "generation": "generated"
        }, {
          "title": "Example - Observation for a single HLA-A allele",
          "nameUrl": "obs-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": "Artifact List",
        "nameUrl": "artifacts.html",
        "generation": "html"
      }, {
        "title": "HL7 Domain Analysis Use Cases",
        "nameUrl": "usecases.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 genetic issues"
    }, {
      "id": "pharmacogenomics",
      "name": "Pharmacogenomics",
      "description": "Profiles for reports relating to genetic impact on medication use and effectiveness"
    }, {
      "id": "cytogenomics",
      "name": "Cytogenomics",
      "description": "Profiles for reporting cytogenetic results"
    }, {
      "id": "extensions",
      "name": "Extensions",
      "description": "Extensions defined as part of the CG implementation guide"
    }, {
      "id": "examples",
      "name": "Example(s)",
      "description": "Example(s) showing the use of the CG profiles"
    }, {
      "id": "device-profile-spreadsheet.xml",
      "name": "Device"
    }, {
      "id": "diagnosticreport-profile-spreadsheet.xml",
      "name": "Genomics Report"
    }, {
      "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/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/diagnosticreport"
    }, {
      "name": "Example - Pharmacogenomics",
      "extension": [ {
        "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/diagnosticreport"
    }, {
      "name": "Example - Full Bundle HLA genotyping for HLA-A, HLA-B, and HLA-C, using GLStrings",
      "extension": [ {
        "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/diagnosticreport"
    }, {
      "name": "Example - HLA genotyping for HLA-A, HLA-B, and HLA-C, using GLStrings",
      "extension": [ {
        "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/diagnosticreport"
    }, {
      "name": "Example - HLA genotyping for HLA-A, using GLStrings",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-genotype-hla-a-glstring-r4.html"
      } ],
      "reference": {
        "reference": "Observation/obs-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/obs-genotype"
    }, {
      "name": "Example - Observation for a single HLA-A allele",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-haplotype-hla-a-1-r4.html"
      } ],
      "reference": {
        "reference": "Observation/obs-haplotype-hla-a-1-r4"
      },
      "groupingId": "examples",
      "description": "HLA-A allele observaation: HLA-A*03:01:01:01",
      "exampleCanonical": "StructureDefinition/obs-haplotype"
    }, {
      "name": "Example - Buccal swab for HLA typing",
      "extension": [ {
        "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/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": "Device Microarray Platform",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "device-micro-plat.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/device-micro-plat"
      },
      "groupingId": "device-profile-spreadsheet.xml"
    }, {
      "name": "Device FISH Probe",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "device-fish-probe.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/device-fish-probe"
      },
      "groupingId": "device-profile-spreadsheet.xml"
    }, {
      "name": "Supporting Information",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "extension-dr-supportingInfo.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/dr-supportingInfo"
      },
      "groupingId": "diagnosticreport-profile-spreadsheet.xml"
    }, {
      "name": "Recommended Action",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "extension-dr-recommendedAction.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/dr-recommendedAction"
      },
      "groupingId": "diagnosticreport-profile-spreadsheet.xml"
    }, {
      "name": "Related Artifact",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "extension-dr-relatedArtifact.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/dr-relatedArtifact"
      },
      "groupingId": "diagnosticreport-profile-spreadsheet.xml"
    }, {
      "name": "Genomics Report",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "diagnosticreport.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/diagnosticreport"
      },
      "groupingId": "diagnosticreport-profile-spreadsheet.xml"
    }, {
      "name": "Current Medication",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "medicationstatement.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/medicationstatement"
      },
      "groupingId": "medicationstatement-profile-spreadsheet.xml"
    }, {
      "name": "GeneticCoordinateSystem",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "valueset-genetic-coordinate-system.html"
      } ],
      "reference": {
        "reference": "ValueSet/genetic-coordinate-system"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "GeneticCoordinateSystem",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "genetic-coordinate-system.html"
      } ],
      "reference": {
        "reference": "CodeSystem/genetic-coordinate-system"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Focus",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "extension-obs-focus.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-focus"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Recommended Action",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "extension-obs-recommendedAction.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-recommendedAction"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Genetic Observation Common Properties",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-base.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-base"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Genomics Panel",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-gen-panel.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-gen-panel"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Genomic analysis overall interpretation",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-overall.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-overall"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Deletion-duplication overall interpretation",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-deletion-dup.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-deletion-dup"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Computable Genetic Finding",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-comp-gen-finding.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-comp-gen-finding"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Genotype",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-genotype.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-genotype"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Haplotype",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-haplotype.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-haplotype"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Complex variation",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-complex-variant.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-complex-variant"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Described Variant",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-described-variant.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-described-variant"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Cytogenetic Nomenclature",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-cytogenetic-nomenclature.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-cytogenetic-nomenclature"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Sequence Phase Relationship",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-sequence-phase-reltn.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-sequence-phase-reltn"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Genomic Impact",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-impact.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-impact"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Inherited Disease Pathogenicity",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-inh-dis-path.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-inh-dis-path"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Medication Impact",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-med-impact.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-med-impact"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Medication Metabolism Impact",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-metabolism.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-metabolism"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Medication Transporter Impact",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-transporter.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-transporter"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Medication Efficacy Impact",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-efficacy.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-efficacy"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "High Risk Allele",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-high-risk.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-high-risk"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Somatic Impact",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-som-impact.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/obs-som-impact"
      },
      "groupingId": "observation-profile-spreadsheet.xml"
    }, {
      "name": "Somatic Diagnostic Impact",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "obs-som-diagnostic.html"
      } ],
      "reference": {
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