Obs-genetics-example1-somatic.json

Genetics Observation of Somatic Variant in Lung Cancer

{
  "resourceType": "Observation",
  "id": "genetics-example1-somatic",
  "text": {
    "status": "generated",
    "div": "<div>!-- Snipped for Brevity --></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"
          }
        ]
      },
      "clinicalStatus": "working"
    }
  ],
  "extension": [
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsGenomeBuild",
      "valueString": "GRCh 37"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsChromosome",
      "valueString": "7"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsGenomicReferenceSequenceId",
      "valueCode": "NC_000007.13"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsGenomicStart",
      "valueInteger": 55259515
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsGenomicStop",
      "valueInteger": 55259515
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsReferenceAllele",
      "valueString": "T"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsObservedAllele",
      "valueString": "G"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsGeneId",
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://www.genenames.org",
            "code": "3236",
            "display": "EGFR"
          }
        ]
      }
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsTranscriptReferenceSequenseId",
      "valueCode": "ENSESTT00000085772.1"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsDNASequenceVariation",
      "valueString": "c.2573T>G"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsVariationId",
      "valueCode": "COSM12979G"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsDNARegionName",
      "valueString": "Exon 21"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsDNASequenceVariationType",
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA6690-7",
            "display": "Substitution"
          }
        ]
      }
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsProteinReferenceSequenceId",
      "valueCode": "ENSESTP00000085772.1"
    },
    {
      "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"
          }
        ]
      }
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsSpecies",
      "valueString": "Human"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsCIGAR",
      "valueString": "GATTTTGGGCtGGCCAAACTG"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/geneticsAssessedCondition",
      "valueReference": {
        "reference": "#c1"
      }
    }
  ],
  "code": {
    "coding": [
      {
        "system": "http://loinc.org",
        "code": "21665-5",
        "display": "EGFR gene mutation analysis"
      }
    ]
  },
  "comments": "The EGFR p.L858R mutation has been associated with response to anti-EGFR therapy",
  "status": "final",
  "subject": {
    "reference": "Patient/genetics-example1-somatic",
    "display": "Molecular Lab Patient ID: HOSP-23456"
  },
  "specimen": {
    "reference": "Specimen/genetics-example1-somatic",
    "display": "Molecular Specimen ID: MLD45-Z4-1234"
  },
  "performer": [
    {
      "reference": "Practitioner/genetics-example1-somatic",
      "display": "Molecular Diagnostic Laboratory"
    }
  ]
}