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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:\u00a0?ngen-9?\u00a0(use:\u00a0OFFICIAL)</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 style=\"display: none\">-</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 style=\"display: none\">*</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 style=\"display: none\">-</td><td><b>Start</b></td><td><b>End</b></td><td><b>ReplacementSequence</b></td><td><b>ReplacedSequence</b></td></tr><tr><td style=\"display: none\">*</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.