Genomics Reporting Implementation Guide
1.1.0 - Ballot

This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

: Example - Inherited Disease Pathogenicity - JSON Representation

Raw json | Download


{
  "resourceType" : "Observation",
  "id" : "obs-idh-ex",
  "meta" : {
    "profile" : [
      "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"
    ]
  },
  "text" : {
    "status" : "extensions",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p><b>Related Artifact</b>: </p><p><b style=\"color: maroon\">Exception generating Narrative: type org.hl7.fhir.r5.model.RelatedArtifact not handled - should not be here</b></p></div>"
  },
  "extension" : [
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/CGRelatedArtifact",
      "valueRelatedArtifact" : {
        "type" : "citation",
        "url" : "https://www.ncbi.nlm.nih.gov/clinvar/variation/53685/#clinical-assertions"
      }
    }
  ],
  "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/TbdCodes",
        "code" : "diagnostic-implication",
        "display" : "Diagnostic Implication"
      }
    ]
  },
  "derivedFrom" : [
    {
      "reference" : "Observation/SNVexample"
    }
  ],
  "component" : [
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "53037-8",
            "display" : "Genetic variation clinical significance [Imp]"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "LA6668-3",
            "display" : "Pathogenic"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "81259-4",
            "display" : "Associated phenotype"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://www.ncbi.nlm.nih.gov/medgen",
            "code" : "C0010674",
            "display" : "Cystic fibrosis"
          },
          {
            "system" : "http://www.orpha.net",
            "code" : "ORPHA:586"
          },
          {
            "system" : "http://www.omim.org",
            "code" : "219700"
          }
        ],
        "text" : "Cystic fibrosis"
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes",
            "code" : "condition-inheritance"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/ConditionInheritanceMode",
            "code" : "HP:0000007",
            "display" : "Autosomal recessive inheritance"
          }
        ]
      }
    }
  ]
}