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Sequence-complex-variant.xml

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

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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 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> </text> <identifier> 
    <use value="official"/> 
  </identifier> 
    <type value="dna"/> 
    <coordinateSystem value="1"/> 
      <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> 
  <quantity> 
  <value value="25"/> 
  </quantity> 
    <referenceSeq> 
        <referenceSeqId> 
          <coding> 
            <system value="http://www.ncbi.nlm.nih.gov/nuccore"/> 
            <code value="NC_000002.12"/> 
          </coding> 
        </referenceSeqId> 
        <strand value="watson"/> 
        <windowStart value="128273724"/> 
        <windowEnd value="128273754"/> 
    </referenceSeq> 
    <variant> 
        <start value="128273724"/> 
        <end value="128273736"/> 
        <observedAllele value="CTCATTGT"/> 
        <referenceAllele value="CTCCATTGCATGCGTT"/> 
        <cigar value="3M1D4M6N2M"/> 
    </variant> 
    <readCoverage value="1"/> 
      <repository> 
      <type value="other"/> 
      <datasetId value="Ensembl"/> 
     <readsetId value="v1beta2"/> 
    </repository> 
    
</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.