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Sequence-complex-variant.json

Clinical Genomics Work GroupMaturity Level: N/AStandards Status: InformativeCompartments: Patient

Raw JSON (canonical form + also see JSON Format Specification)

Example of representing complex variants in MolecularSequence resource

{
  "resourceType": "MolecularSequence",
  "id": "sequence-complex-variant",
  "text": {
    "status": "generated",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: sequence-complex-variant</p><p><b>identifier</b>: ?? (OFFICIAL)</p><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 1</p><p><b>specimen</b>: <a>Molecular Specimen ID: MLD45-Z4-1234</a></p><p><b>device</b>: 12 lead EKG Device Metric</p><p><b>performer</b>: <a>HL7</a></p><p><b>quantity</b>: 25</p><h3>ReferenceSeqs</h3><table><tr><td>-</td><td><b>ReferenceSeqId</b></td><td><b>Strand</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>NC_000002.12 <span>(Details : {http://www.ncbi.nlm.nih.gov/nuccore code 'NC_000002.12' = 'NC_000002.12)</span></td><td>watson</td><td>128273724</td><td>128273754</td></tr></table><h3>Variants</h3><table><tr><td>-</td><td><b>Start</b></td><td><b>End</b></td><td><b>ObservedAllele</b></td><td><b>ReferenceAllele</b></td><td><b>Cigar</b></td></tr><tr><td>*</td><td>128273724</td><td>128273736</td><td>CTCATTGT</td><td>CTCCATTGCATGCGTT</td><td>3M1D4M6N2M</td></tr></table><p><b>readCoverage</b>: 1</p><h3>Repositories</h3><table><tr><td>-</td><td><b>Type</b></td><td><b>DatasetId</b></td><td><b>ReadsetId</b></td></tr><tr><td>*</td><td>other</td><td>Ensembl</td><td>v1beta2</td></tr></table></div>"
  },
  "identifier": [
    {
      "use": "official"
    }
  ],
  "type": "dna",
  "coordinateSystem": 1,
  "specimen": {
    "reference": "Specimen/genetics-example1-somatic",
    "display": "Molecular Specimen ID: MLD45-Z4-1234"
  },
  "device": {
    "display": "12 lead EKG Device Metric"
  },
  "performer": {
    "reference": "Organization/hl7",
    "display": "HL7"
  },
  "quantity": {
    "value": 25
  },
  "referenceSeq": {
    "referenceSeqId": {
      "coding": [
        {
          "system": "http://www.ncbi.nlm.nih.gov/nuccore",
          "code": "NC_000002.12"
        }
      ]
    },
    "strand": "watson",
    "windowStart": 128273724,
    "windowEnd": 128273754
  },
  "variant": [
    {
      "start": 128273724,
      "end": 128273736,
      "observedAllele": "CTCATTGT",
      "referenceAllele": "CTCCATTGCATGCGTT",
      "cigar": "3M1D4M6N2M"
    }
  ],
  "readCoverage": 1,
  "repository": [
    {
      "type": "other",
      "datasetId": "Ensembl",
      "readsetId": "v1beta2"
    }
  ]
}

Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.