Observation-example-genetics-1.json

Genetics Observation of Somatic Variant in Lung Cancer

{
  "resourceType": "Observation",
  "id": "ob-genetics-1",
  "text": {
    "status": "generated",
    "div": "<div><p><b>Generated Narrative with Details</b></p><p><b>id</b>: ob-genetics-1</p><p><b>status</b>: final</p><p><b>code</b>: Genetic analysis master panel <span>(Details : {LOINC code '55233-1' = 'Genetic analysis master panel - Blood or Tissue by Molecular genetics method', given as 'Genetic analysis master panel'})</span></p><p><b>subject</b>: <a>Molecular Lab Patient ID: HOSP-23456</a></p><p><b>issued</b>: 11/03/2013 10:28:00 AM</p><p><b>performer</b>: <a>Molecular Diagnostic Laboratory</a></p><p><b>value</b>: Positive <span>(Details : {SNOMED CT code '10828004' = '10828004', given as 'Positive'})</span></p><p><b>specimen</b>: <a>Molecular Specimen ID: MLD45-Z4-1234</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Genetic disease assessed <span>(Details : {LOINC code '51967-8' = 'Genetic disease assessed [Identifier] in Blood or Tissue by Molecular genetics method', given as 'Genetic disease assessed'})</span></p><p><b>value</b>: Lung cancer <span>(Details : {SNOMED CT code '363358000' = '??', given as 'Malignant tumor of lung (disorder)'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genetic disease sequence variation interpretation <span>(Details : {LOINC code '53037-8' = 'Genetic disease sequence variation interpretation [interpretation] in Blood or Tissue by Molecular genetics method', given as 'Genetic disease sequence variation interpretation'})</span></p><p><b>value</b>: Pathogenic <span>(Details : {[not stated] code 'LA6669-1' = '??', given as 'Pathogenic'})</span></p></blockquote></div>"
  },
  "extension": [
    {
      "url": "http://hl7.org/fhir/StructureDefinition/observation-geneticsSequence",
      "valueReference": {
        "reference": "Sequence/example"
      }
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/observation-geneticsSource",
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/LOINC-48002-0-answerlist",
            "code": "LA6684-0",
            "display": "somatic"
          }
        ]
      }
    },
    {
      "extension": [
        {
          "url": "genomeBuild",
          "valueCodeableConcept": {
            "text": "GRCh 38"
          }
        },
        {
          "url": "name",
          "valueCodeableConcept": {
            "text": "NG_007726.3:g.146252T>G"
          }
        }
      ],
      "url": "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariationHGVS"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/observation-geneticsGene",
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://www.genenames.org",
            "code": "3236",
            "display": "EGFR"
          }
        ]
      }
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/observation-geneticsRegion",
      "valueCodeableConcept": {
        "text": "Exon 21"
      }
    }
  ],
  "status": "final",
  "code": {
    "coding": [
      {
        "system": "http://loinc.org",
        "code": "55233-1",
        "display": "Genetic analysis master panel"
      }
    ]
  },
  "subject": {
    "reference": "Patient/genetics-example1-somatic",
    "display": "Molecular Lab Patient ID: HOSP-23456"
  },
  "issued": "2013-03-11T10:28:00+01:00",
  "performer": [
    {
      "reference": "Practitioner/genetics-example1-somatic",
      "display": "Molecular Diagnostic Laboratory"
    }
  ],
  "valueCodeableConcept": {
    "coding": [
      {
        "system": "http://snomed.info/sct",
        "code": "10828004",
        "display": "Positive"
      }
    ]
  },
  "specimen": {
    "reference": "Specimen/genetics-example1-somatic",
    "display": "Molecular Specimen ID: MLD45-Z4-1234"
  },
  "component": [
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "51967-8",
            "display": "Genetic disease assessed"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://snomed.info/sct",
            "code": "363358000",
            "display": "Malignant tumor of lung (disorder)"
          }
        ],
        "text": "Lung cancer"
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "53037-8",
            "display": "Genetic disease sequence variation interpretation"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "code": "LA6669-1",
            "display": "Pathogenic"
          }
        ]
      }
    }
  ]
}