Release 5 Ballot

This page is part of the FHIR Specification (v5.0.0-ballot: R5 Ballot - see ballot notes). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions . Page versions: R5 R4B R4 R3

Example MolecularSequence/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: MolecularSequence</b><a name=\"sequence-complex-variant\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource MolecularSequence &quot;sequence-complex-variant&quot; </p></div><p><b>identifier</b>: id: ?ngen-9? (OFFICIAL)</p><p><b>type</b>: dna</p><p><b>specimen</b>: <a href=\"broken-link.html\">Specimen/genetics-example1-somatic: Molecular Specimen ID: MLD45-Z4-1234</a></p><p><b>device</b>: <span>: 12 lead EKG Device Metric</span></p><p><b>performer</b>: <a href=\"organization-example.html\">Organization/hl7: HL7</a> &quot;Health Level Seven International&quot;</p><blockquote><p><b>relative</b></p><p><b>coordinateSystem</b>: 0-based interval counting <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA30100-4)</span></p><h3>StartingSequences</h3><table class=\"grid\"><tr><td>-</td><td><b>Sequence[x]</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td><td><b>Strand</b></td></tr><tr><td>*</td><td>NC_000002.12 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (nuccore#NC_000002.12)</span></td><td>128273724</td><td>128273754</td><td>watson</td></tr></table><h3>Edits</h3><table class=\"grid\"><tr><td>-</td><td><b>Start</b></td><td><b>End</b></td><td><b>ReplacementSequence</b></td><td><b>ReplacedSequence</b></td></tr><tr><td>*</td><td>128273724</td><td>128273736</td><td>CTCATTGT</td><td>CTCCATTGCATGCGTT</td></tr></table></blockquote></div>"
  },
  "identifier": [
    {
      "use": "official"
    }
  ],
  "type": "dna",
  "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"
  },
  "relative": [
    {
      "coordinateSystem": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA30100-4",
            "display": "0-based interval counting"
          }
        ]
      },
      "startingSequence": {
        "sequenceCodeableConcept": {
          "coding": [
            {
              "system": "http://www.ncbi.nlm.nih.gov/nuccore",
              "code": "NC_000002.12"
            }
          ]
        },
        "windowStart": 128273724,
        "windowEnd": 128273754,
        "strand": "watson"
      },
      "edit": [
        {
          "start": 128273724,
          "end": 128273736,
          "replacementSequence": "CTCATTGT",
          "replacedSequence": "CTCCATTGCATGCGTT"
        }
      ]
    }
  ]
}

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.