Obs-genetics-example1-somatic.json

Genetics Observation of Somatic Variant in Lung Cancer

{
  "resourceType": "Observation",
  "id": "genetics-example1-somatic",
  "text": {
    "status": "generated",
    "div": "<div><p><b>Generated Narrative with Details</b></p><p><b>id</b>: genetics-example1-somatic</p><p><b>contained</b>: </p><p><b>status</b>: final</p><p><b>code</b>: Genetic analysis master panel ­Blood or Tissue by Molecular genetics method <span>(Details : {LOINC code '55233-1' = 'Genetic analysis master panel - Blood or Tissue by Molecular genetics method', given as 'Genetic analysis master panel ­Blood or Tissue by Molecular genetics method'})</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>interpretation</b>: positive <span>(Details : {http://hl7.org/fhir/v2/0078 code 'POS' = 'Positive)</span></p><p><b>comments</b>: The EGFR p.L858R mutation has been associated with response to anti-EGFR therapy</p><p><b>specimen</b>: <a>Molecular Specimen ID: MLD45-Z4-1234</a></p></div>"
  },
  "contained": [
    {
      "resourceType": "Condition",
      "id": "c1",
      "patient": {
        "reference": "Patient/p1"
      },
      "code": {
        "coding": [
          {
            "system": "http://snomed.info/sct",
            "code": "254626006"
          }
        ],
        "text": "Adenocarcinoma of lung "
      },
      "category": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/condition-category",
            "code": "finding",
            "display": "Finding"
          }
        ]
      },
      "verificationStatus": "provisional"
    }
  ],
  "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_000007"
          }
        ],
        "text": "Homo sapiens chromosome 7"
      }
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsGenomicStart",
      "valueInteger": 55259515
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsGenomicStop",
      "valueInteger": 55259516
    },
    {
      "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"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsAssessedCondition",
      "valueReference": {
        "reference": "#c1"
      }
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsReferenceAllele",
      "valueString": "T"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsObservedAllele",
      "valueString": "G"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsGene",
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://www.genenames.org",
            "code": "3236",
            "display": "EGFR"
          }
        ]
      }
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsTranscriptReferenceSequenceId",
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://www.ensembl.org",
            "code": "ENSESTT00000085772.1"
          }
        ]
      }
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsDNASequenceVariation",
      "valueString": "c.2573T>G"
    },
    {
      "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.Leu858Arg"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsAlleleName",
      "valueString": "p.L858R"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsGenomicSourceClass",
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA6684-0",
            "display": "Somatic"
          }
        ]
      }
    }
  ],
  "status": "final",
  "code": {
    "coding": [
      {
        "system": "http://loinc.org",
        "code": "55233-1",
        "display": "Genetic analysis master panel ­Blood or Tissue by Molecular genetics method"
      }
    ]
  },
  "subject": {
    "reference": "Patient/genetics-example1-somatic",
    "display": "Molecular Lab Patient ID: HOSP-23456"
  },
  "performer": [
    {
      "reference": "Practitioner/genetics-example1-somatic",
      "display": "Molecular Diagnostic Laboratory"
    }
  ],
  "interpretation": {
    "coding": [
      {
        "system": "http://hl7.org/fhir/v2/0078",
        "code": "POS"
      }
    ],
    "text": "positive"
  },
  "comments": "The EGFR p.L858R mutation has been associated with response to anti-EGFR therapy",
  "specimen": {
    "reference": "Specimen/genetics-example1-somatic",
    "display": "Molecular Specimen ID: MLD45-Z4-1234"
  }
}