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

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: Example - NGS - JSON Representation

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{
  "resourceType" : "Observation",
  "id" : "SNVexample",
  "meta" : {
    "profile" : [
      "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
    ]
  },
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p></p><p><b>category</b>: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 69548-6}\">Genetic variant assessment</span></p><p><b>value</b>: <span title=\"Codes: {http://loinc.org LA9633-4}\">Present</span></p><p><b>method</b>: <span title=\"Codes: {http://loinc.org LA26398-0}\">Sequencing</span></p><p><b>specimen</b>: <span></span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 48018-6}\">Gene studied ID</span></p><p><b>value</b>: <span title=\"Codes: {http://www.genenames.org/geneId HGNC:644}\">AR</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 48001-2}\">Cytogenetic (chromosome) location</span></p><p><b>value</b>: <span title=\"Codes: \">chrX</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 62374-4}\">Human reference sequence assembly version</span></p><p><b>value</b>: <span title=\"Codes: {http://loinc.org LA14029-5}\">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 48002-0}\">Genomic source class</span></p><p><b>value</b>: <span title=\"Codes: {http://loinc.org LA6684-0}\">Somatic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 48005-3}\">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title=\"Codes: {http://varnomen.hgvs.org p.(Ala412Val)}\">p.(Ala412Val)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 48006-1}\">Amino acid change type</span></p><p><b>value</b>: <span title=\"Codes: {http://loinc.org LA6698-0}\">Missense</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 51958-7}\">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes: {http://www.ncbi.nlm.nih.gov/refseq NM_000044.3}\">NM_000044.3</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 81258-6}\">Sample VAF</span></p><p><b>value</b>: 0.44 decimal</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 82121-5}\">Allelic read depth</span></p><p><b>value</b>: 120 reads per base pair</p></blockquote></div>"
  },
  "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"
      }
    ]
  },
  "valueCodeableConcept" : {
    "coding" : [
      {
        "system" : "http://loinc.org",
        "code" : "LA9633-4",
        "display" : "Present"
      }
    ]
  },
  "method" : {
    "coding" : [
      {
        "system" : "http://loinc.org",
        "code" : "LA26398-0",
        "display" : "Sequencing"
      }
    ]
  },
  "specimen" : {
    "identifier" : {
      "system" : "http://slk-kliniken.de/fhir/namingSystem/tissueID",
      "value" : "16-123456-23"
    }
  },
  "component" : [
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "48018-6",
            "display" : "Gene studied ID"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://www.genenames.org/geneId",
            "code" : "HGNC:644",
            "display" : "AR"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "48001-2",
            "display" : "Cytogenetic (chromosome) location"
          }
        ]
      },
      "valueCodeableConcept" : {
        "text" : "chrX"
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "62374-4",
            "display" : "Human reference sequence assembly version"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "LA14029-5",
            "display" : "GRCh37"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "48002-0",
            "display" : "Genomic source class"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "LA6684-0",
            "display" : "Somatic"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "48005-3",
            "display" : "Amino acid change (pHGVS)"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://varnomen.hgvs.org",
            "code" : "p.(Ala412Val)",
            "display" : "p.(Ala412Val)"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "48006-1",
            "display" : "Amino acid change type"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "LA6698-0",
            "display" : "Missense"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "51958-7",
            "display" : "Transcript reference sequence [ID]"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://www.ncbi.nlm.nih.gov/refseq",
            "code" : "NM_000044.3",
            "display" : "NM_000044.3"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "81258-6",
            "display" : "Sample VAF"
          }
        ]
      },
      "valueQuantity" : {
        "value" : 0.44,
        "unit" : "decimal",
        "system" : "http://unitsofmeasure.org"
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "82121-5",
            "display" : "Allelic read depth"
          }
        ]
      },
      "valueQuantity" : {
        "value" : 120,
        "unit" : "reads per base pair",
        "system" : "http://unitsofmeasure.org",
        "code" : "{reads}/{base}"
      }
    }
  ]
}