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FHIR IG analytics

Packagehl7.fhir.uv.genomics-reporting
Resource TypeObservation
IdObservation-pop-allele-freq.json
FHIR VersionR4

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Narrative

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

Generated Narrative: Observation pop-allele-freq

status: Final

category: Laboratory, Genetics

code: Genomic Annotation

subject: Alanine B. Everyone Unknown, DoB: 1951-01-20 ( Medical Record Number: m234 (use: usual, ))

effective: 2023-06-01

performer: Organization Some lab

derivedFrom: Observation Genetic variant assessment

component

Knowledgebase Ancestry Group: south asian

code: Allelic frequency in Population

value: 0.01

component

code: Knowledge Base

value: gnomAD v3.1.2 Exomes

component

code: Annotation Pipeline

value: Oakvar v2.34

Source1

{
  "resourceType": "Observation",
  "id": "pop-allele-freq",
  "meta": {
    "profile": [
      "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-annotation"
    ]
  },
  "text": {
    "status": "extensions",
    "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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
        "code": "genomic-annotation"
      }
    ]
  },
  "subject": {
    "reference": "Patient/HG00403"
  },
  "effectiveDateTime": "2023-06-01",
  "performer": [
    {
      "reference": "Organization/ExampleLab"
    }
  ],
  "derivedFrom": [
    {
      "reference": "Observation/variant-with-molec-consequences"
    }
  ],
  "component": [
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group",
          "valueCodeableConcept": {
            "text": "south asian"
          }
        }
      ],
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "92821-8",
            "display": "Allelic frequency in Population"
          }
        ]
      },
      "valueQuantity": {
        "value": 0.01
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
            "code": "knowledge-base"
          }
        ]
      },
      "valueCodeableConcept": {
        "text": "gnomAD v3.1.2 Exomes"
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
            "code": "annotation-pipeline"
          }
        ]
      },
      "valueCodeableConcept": {
        "text": "Oakvar v2.34"
      }
    }
  ]
}