Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

: EGFR-L858R-var - JSON Representation

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{
  "resourceType" : "Observation",
  "id" : "EGFR-L858R-var",
  "meta" : {
    "profile" : [
      🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
    ]
  },
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation EGFR-L858R-var</b></p><a name=\"EGFR-L858R-var\"> </a><a name=\"hcEGFR-L858R-var\"> </a><a name=\"EGFR-L858R-var-en-US\"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></p><p><b>subject</b>: <a href=\"Patient-somaticPatient.html\">Substance Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567\u00a0(use:\u00a0temp,\u00a0period:\u00a02021-01-01 --&gt; (ongoing)))</a></p><p><b>effective</b>: 2023-02-01</p><p><b>performer</b>: <a href=\"Practitioner-pathologistPractitioner.html\">Practitioner Test Dolin </a></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><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81252-9}\">Discrete genetic variant</span></p><p><b>value</b>: <span title=\"Codes:\">EGFR L858R</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 NP_005219.2:p.Leu858Arg}\">NP_005219.2:p.Leu858Arg</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48019-4}\">DNA change type</span></p><p><b>value</b>: <span title=\"Codes:{http://sequenceontology.org SO:0001483}\">SNV</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48004-6}\">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NM_005228.4:c.2573T&gt;G}\">NM_005228.4:c.2573T&gt;G</span></p></blockquote><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 HGNC:3236}\">EGFR</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81290-9}\">Genomic DNA change (gHGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NC_000007.13:g.55259515T&gt;G}\">NC_000007.13:g.55259515T&gt;G</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48002-0}\">Genomic source class [Type]</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 81258-6}\">Sample variant allelic frequency [NFr]</span></p><p><b>value</b>: 0.066 decimal</p></blockquote></div>"
  },
  "status" : "final",
  "category" : [
    {
      "coding" : [
        {
          "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
          "code" : "laboratory"
        }
      ]
    },
    {
      "coding" : [
        {
          "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
          "code" : "GE"
        }
      ]
    }
  ],
  "code" : {
    "coding" : [
      {
        "system" : "http://loinc.org",
        "code" : "69548-6"
      }
    ]
  },
  "subject" : {
    🔗 "reference" : "Patient/somaticPatient"
  },
  "effectiveDateTime" : "2023-02-01",
  "performer" : [
    {
      🔗 "reference" : "Practitioner/pathologistPractitioner"
    }
  ],
  "valueCodeableConcept" : {
    "coding" : [
      {
        "system" : "http://loinc.org",
        "code" : "LA9633-4",
        "display" : "Present"
      }
    ]
  },
  "method" : {
    "coding" : [
      {
        "system" : "http://loinc.org",
        "code" : "LA26398-0",
        "display" : "Sequencing"
      }
    ]
  },
  "component" : [
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "81252-9"
          }
        ]
      },
      "valueCodeableConcept" : {
        "text" : "EGFR L858R"
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "48005-3"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://varnomen.hgvs.org",
            "code" : "NP_005219.2:p.Leu858Arg"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "48019-4"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://sequenceontology.org",
            "code" : "SO:0001483",
            "display" : "SNV"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "48004-6"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://varnomen.hgvs.org",
            "code" : "NM_005228.4:c.2573T>G"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "48018-6"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://www.genenames.org",
            "code" : "HGNC:3236",
            "display" : "EGFR"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "81290-9"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://varnomen.hgvs.org",
            "code" : "NC_000007.13:g.55259515T>G"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "48002-0"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "LA6684-0",
            "display" : "Somatic"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "81258-6"
          }
        ]
      },
      "valueQuantity" : {
        "value" : 0.066,
        "unit" : "decimal",
        "system" : "http://unitsofmeasure.org"
      }
    }
  ]
}