Obs-genetics-example2-germline.json

Genetics Observation of Germline BRCA1 Variant

{
  "resourceType": "Observation",
  "id": "genetics-example2-germline",
  "text": {
    "status": "generated",
    "div": "<div><p><b>Generated Narrative with Details</b></p><p><b>id</b>: genetics-example2-germline</p><p><b>status</b>: final</p><p><b>code</b>: BRCA1 gene mutation analysis <span>(Details : {LOINC code '21636-6' = 'BRCA1 gene mutations found [Identifier] in Blood or Tissue by Molecular genetics method Nominal', given as 'BRCA1 gene mutation analysis'})</span></p><p><b>subject</b>: <a>Molecular Lab Patient ID: HOSP-23456</a></p><p><b>performer</b>: <a>Molecular Diagnostic Laboratory</a></p><p><b>specimen</b>: <a>Molecular Specimen ID: MLD45-Z4-1234</a></p></div>"
  },
  "extension": [
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsGenomeBuild",
      "valueString": "GRCh 37"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsChromosome",
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://www.ncbi.nlm.nih.gov/gene",
            "code": "NC_000017"
          }
        ],
        "text": "Homo sapiens chromosome 17"
      }
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsGenomicStart",
      "valueInteger": 41258504
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsGenomicStop",
      "valueInteger": 41258505
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsReferenceAllele",
      "valueString": "A"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsObservedAllele",
      "valueString": "C"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsGene",
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://www.genenames.org",
            "code": "1100",
            "display": "BRCA1"
          }
        ]
      }
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsDNASequenceVariation",
      "valueString": "c.181T>G"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsVariationId",
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://www.ncbi.nlm.nih.gov/clinvar",
            "code": "17661",
            "display": "c.181T>G"
          }
        ]
      }
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsDNARegionName",
      "valueString": "Exon 4"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsDNASequenceVariationType",
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA6690-7",
            "display": "Substitution"
          }
        ]
      }
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsAminoAcidChange",
      "valueString": "p.Cys61Gly"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsGenomicSourceClass",
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA6683-2",
            "display": "Germline"
          }
        ]
      }
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsSpecies",
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://snomed.info/sct",
            "code": "337915000"
          }
        ],
        "text": "Homo sapiens"
      }
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsCIGAR",
      "valueString": "1M"
    }
  ],
  "status": "final",
  "code": {
    "coding": [
      {
        "system": "http://loinc.org",
        "code": "21636-6",
        "display": "BRCA1 gene mutation analysis"
      }
    ]
  },
  "subject": {
    "reference": "Patient/genetics-example2-germline",
    "display": "Molecular Lab Patient ID: HOSP-23456"
  },
  "performer": [
    {
      "reference": "Practitioner/genetics-example2-germline",
      "display": "Molecular Diagnostic Laboratory"
    }
  ],
  "specimen": {
    "reference": "Specimen/genetics-example2-germline",
    "display": "Molecular Specimen ID: MLD45-Z4-1234"
  }
}