Observation-consensus-sequence-block-example-1.json

Example of HLA genotyping results - consensus sequence block 1

{
  "resourceType": "Observation",
  "id": "consensus-sequence-block-example-1",
  "text": {
    "status": "generated",
    "div": "<div><p><b>Generated Narrative with Details</b></p><p><b>id</b>: consensus-sequence-block-example-1</p><p><b>contained</b>: , </p><p><b>status</b>: final</p><p><b>code</b>: HLA-A [Type] <span>(Details : {LOINC code '13298-5' = 'HLA-A [Type])</span></p></div>"
  },
  "contained": [
    {
      "resourceType": "Sequence",
      "id": "variant-1",
      "type": "DNA",
      "coordinate": [
        {
          "start": 29945809,
          "end": 29942810
        }
      ],
      "observedAllele": "AT",
      "referenceAllele": "C"
    },
    {
      "resourceType": "Sequence",
      "id": "variant-2",
      "type": "DNA",
      "coordinate": [
        {
          "start": 29942940,
          "end": 29942942
        }
      ],
      "observedAllele": "G",
      "referenceAllele": "CT"
    }
  ],
  "extension": [
    {
      "url": "http://hl7.org/fhir/StructureDefinition/observation-consensus-sequence-blockReferenceSeq",
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/",
            "code": "ref1"
          }
        ]
      }
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/observation-consensus-sequence-blockStart",
      "valueInteger": 29942412
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/observation-consensus-sequence-blockEnd",
      "valueInteger": 29942852
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/observation-consensus-sequence-blockPhaseSet",
      "valueInteger": 1
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/observation-consensus-sequence-blockExpectedCopyNumber",
      "valueInteger": 1
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/observation-consensus-sequence-blockContinuity",
      "valueBoolean": true
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/observation-consensus-sequence-blockVariant",
      "valueReference": {
        "reference": "#variant-1"
      }
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/observation-consensus-sequence-blockVariant",
      "valueReference": {
        "reference": "#variant-2"
      }
    }
  ],
  "status": "final",
  "code": {
    "coding": [
      {
        "system": "http://loinc.org",
        "code": "13298-5"
      }
    ]
  }
}