This page is part of the Genetic Reporting Implementation Guide (v1.0.0: STU 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

(back to narrative)

Raw json

{
  "resourceType" : "Observation",
  "id" : "obs-idh-ex",
  "meta" : {
    "profile" : [
      "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/inherited-disease-pathogenicity"
    ]
  },
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: obs-idh-ex</p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow\">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Genetic variation clinical significance [Imp] <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '53037-8' = 'Genetic variation clinical significance [Imp]', given as 'Genetic variation clinical significance [Imp]'})</span></p><p><b>value</b>: Pathogenic <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA6668-3' = 'Pathogenic', given as 'Pathogenic'})</span></p><p><b>derivedFrom</b>: <a href=\"obs-idh-ex.html\">Generated Summary: id: SNVexample; <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>; <span title=\"Codes: {http://loinc.org 69548-6}\">Genetic variant assessment</span>; <span title=\"Codes: {http://loinc.org LA9633-4}\">Present</span>; <span title=\"Codes: {http://loinc.org LA26398-0}\">Sequencing</span></a></p><blockquote><p><b>component</b></p><p><b>code</b>: Associated phenotype <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '81259-4' = 'Associated phenotype', given as 'Associated phenotype'})</span></p><p><b>value</b>: Cystic fibrosis <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.ncbi.nlm.nih.gov/medgen code 'C0010674' = 'C0010674', given as 'Cystic fibrosis'}; {http://www.orpha.net code 'ORPHA:586' = 'ORPHA:586; {http://www.omim.org code '219700' = '219700)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Associated phenotype <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '81259-4' = 'Associated phenotype', given as 'Associated phenotype'})</span></p><p><b>value</b>: Congenital bilateral absence of the vas deferens <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.ncbi.nlm.nih.gov/medgen code 'C0403814' = 'C0403814; {http://www.orpha.net code 'ORPHA:48' = 'ORPHA:48; {http://www.omim.org code '277180' = '277180; {http://www.omim.org code '300985' = '300985)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: mode-of-inheritance <span style=\"background: LightGoldenRodYellow\">(Details : {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes code 'mode-of-inheritance' = 'mode-of-inheritance', given as 'mode-of-inheritance'})</span></p><p><b>value</b>: Autosomal recessive <span style=\"background: LightGoldenRodYellow\">(Details : {http://ghr.nlm.nih.gov/primer/inheritance/inheritancepatterns code 'Autosomal recessive' = 'Autosomal recessive', given as 'Autosomal recessive'})</span></p></blockquote></div>"
  },
  "extension" : [
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/RelatedArtifact",
      "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://loinc.org",
        "code" : "53037-8",
        "display" : "Genetic variation clinical significance [Imp]"
      }
    ]
  },
  "valueCodeableConcept" : {
    "coding" : [
      {
        "system" : "http://loinc.org",
        "code" : "LA6668-3",
        "display" : "Pathogenic"
      }
    ]
  },
  "derivedFrom" : [
    {
      "reference" : "Observation/SNVexample"
    }
  ],
  "component" : [
    {
      "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://loinc.org",
            "code" : "81259-4",
            "display" : "Associated phenotype"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://www.ncbi.nlm.nih.gov/medgen",
            "code" : "C0403814"
          },
          {
            "system" : "http://www.orpha.net",
            "code" : "ORPHA:48"
          },
          {
            "system" : "http://www.omim.org",
            "code" : "277180"
          },
          {
            "system" : "http://www.omim.org",
            "code" : "300985"
          }
        ],
        "text" : "Congenital bilateral absence of the vas deferens"
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes",
            "code" : "mode-of-inheritance",
            "display" : "mode-of-inheritance"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://ghr.nlm.nih.gov/primer/inheritance/inheritancepatterns",
            "code" : "Autosomal recessive",
            "display" : "Autosomal recessive"
          }
        ]
      }
    }
  ]
}