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Example MolecularSequence/sequence-complex-variant (XML)

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

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

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Example of representing complex variants in MolecularSequence resource (id = "sequence-complex-variant")

<?xml version="1.0" encoding="UTF-8"?>

<MolecularSequence xmlns="http://hl7.org/fhir">
    <id value="sequence-complex-variant"/> 
    <text> <status value="generated"/> <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> </text> <identifier> 
      <use value="official"/> 
    </identifier> 
    <type value="dna"/> 
    <specimen> 
      <reference value="Specimen/genetics-example1-somatic"/> 
      <display value="Molecular Specimen ID: MLD45-Z4-1234"/> 
    </specimen> 
    <device> 
      <display value="12 lead EKG Device Metric"/> 
    </device> 
    <performer> 
      <reference value="Organization/hl7"/> 
      <display value="HL7"/> 
    </performer> 
    <relative> 
      <coordinateSystem> 
          <coding> 
              <system value="http://loinc.org"/> 
              <code value="LA30100-4"/> 
              <display value="0-based interval counting"/> 
          </coding> 
      </coordinateSystem> 
      <startingSequence> 
          <sequenceCodeableConcept> 
            <coding> 
              <system value="http://www.ncbi.nlm.nih.gov/nuccore"/> 
              <code value="NC_000002.12"/> 
            </coding> 
          </sequenceCodeableConcept> 
          <windowStart value="128273724"/> 
          <windowEnd value="128273754"/> 
          <strand value="watson"/> 
      </startingSequence> 
      <edit> 
          <start value="128273724"/> 
          <end value="128273736"/> 
          <replacementSequence value="CTCATTGT"/> 
          <replacedSequence value="CTCCATTGCATGCGTT"/> 
      </edit>     
    </relative> 
</MolecularSequence> 

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.