FHIRsmith: Observation/Observation-VariantExample2.json

FHIR IG analytics

Package	hl7.fhir.uv.genomics-reporting.r4b
Resource Type	Observation
Id	Observation-VariantExample2.json
FHIR Version	R4B

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Narrative

Note: links and images are rebased to the (stated) source

Generated Narrative: Observation VariantExample2

status: Final

category: Laboratory, Genetics

code: Genetic variant assessment

subject: Adam B. Everyman Male, DoB: 1951-01-20 ( Medical Record Number: m123 (use: usual, ))

effective: 2019-04-01

performer: Organization some lab

value: Present

method: Sequencing

component
code: Genomic reference sequence [ID]
value: NC_000010.10

component
code: Allelic State
value: heterozygous

component
code: Ref nucleotide
value: C

component
code: Alt allele
value: A

component
code: Genomic allele start-end
value: 96527334-?

Source1

{
  "resourceType": "Observation",
  "id": "VariantExample2",
  "meta": {
    "profile": [
      "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
    ]
  },
  "text": {
    "status": "generated",
    "div": "<!-- snip (see above) -->"
  },
  "status": "final",
  "category": [
    {
      "coding": [
        {
          "system": "http://terminology.hl7.org/CodeSystem/observation-category",
          "code": "laboratory"
        }
      ]
    },
    {
      "coding": [
        {
          "system": "http://terminology.hl7.org/CodeSystem/v2-0074",
          "code": "GE"
        }
      ]
    }
  ],
  "code": {
    "coding": [
      {
        "system": "http://loinc.org",
        "code": "69548-6"
      }
    ]
  },
  "subject": {
    "reference": "Patient/CGPatientExample01"
  },
  "effectiveDateTime": "2019-04-01",
  "performer": [
    {
      "reference": "Organization/ExampleOrg"
    }
  ],
  "valueCodeableConcept": {
    "coding": [
      {
        "system": "http://loinc.org",
        "code": "LA9633-4",
        "display": "Present"
      }
    ]
  },
  "method": {
    "coding": [
      {
        "system": "http://loinc.org",
        "code": "LA26398-0",
        "display": "Sequencing"
      }
    ]
  },
  "component": [
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "48013-7",
            "display": "Genomic reference sequence [ID]"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://www.ncbi.nlm.nih.gov/refseq",
            "code": "NC_000010.10"
          }
        ]
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "53034-5",
            "display": "Allelic State"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA6706-1",
            "display": "heterozygous"
          }
        ]
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "69547-8",
            "display": "Ref nucleotide"
          }
        ]
      },
      "valueString": "C"
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "69551-0",
            "display": "Alt allele"
          }
        ]
      },
      "valueString": "A"
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "81254-5",
            "display": "Genomic allele start-end"
          }
        ]
      },
      "valueRange": {
        "low": {
          "value": 96527334
        }
      }
    }
  ]
}