Observation-example-genetics-6-3.json

Genetics Observation for BRCA1 n.342T>G

{
  "resourceType": "Observation",
  "id": "ob-genetics-6-3",
  "text": {
    "status": "generated",
    "div": "<div><p><b>Generated Narrative with Details</b></p><p><b>id</b>: ob-genetics-6-3</p><p><b>contained</b>: </p><p><b>status</b>: final</p><p><b>code</b>: BRCA1 gene mutations found [Identifier] in Blood or Tissue by Molecular genetics method Nominal <span>(Details : {https://loinc.org/ code '21636-6' = '??', given as 'BRCA1 gene mutations found [Identifier] in Blood or Tissue by Molecular genetics method Nominal'})</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></div>"
  },
  "contained": [
    {
      "resourceType": "Sequence",
      "id": "g-3",
      "type": "DNA",
      "variationID": [
        {
          "coding": [
            {
              "system": "http://www.ncbi.nlm.nih.gov/projects/SNP",
              "code": "28897672"
            }
          ]
        }
      ],
      "referenceSeq": {
        "coding": [
          {
            "system": "http://www.ncbi.nlm.nih.gov/nuccore/",
            "code": "NM_007298.3"
          }
        ]
      },
      "coordinate": [
        {
          "chromosome": {
            "coding": [
              {
                "code": "17"
              }
            ]
          },
          "start": 43106487,
          "end": 43106488,
          "genomeBuild": {
            "text": "GRCh38.p2"
          }
        }
      ],
      "observedAllele": "G",
      "referenceAllele": "T"
    }
  ],
  "extension": [
    {
      "url": "http://hl7.org/fhir/StructureDefinition/observation-geneticsSequence",
      "valueReference": {
        "reference": "#g-3"
      }
    },
    {
      "extension": [
        {
          "url": "genomeBuild",
          "valueCodeableConcept": {
            "text": "GRCh 38"
          }
        },
        {
          "url": "name",
          "valueCodeableConcept": {
            "text": "n.342T>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": "672",
            "display": "BRCA1"
          }
        ]
      }
    }
  ],
  "status": "final",
  "code": {
    "coding": [
      {
        "system": "https://loinc.org/",
        "code": "21636-6",
        "display": "BRCA1 gene mutations found [Identifier] in Blood or Tissue by Molecular genetics method Nominal"
      }
    ]
  },
  "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"
  }
}