Release 4 4B

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Sequence-genetics-example-breastcancer.xml

Clinical Genomics Work Group Maturity Level : N/A Standards Status : Informative Compartments : Patient

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

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MolecularSequence example for patient with breast cancer gene variant (id = "breastcancer") 

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

<MolecularSequence xmlns="http://hl7.org/fhir">
    <id value="breastcancer"/> 
    (Details : {http://www.ncbi.nlm.nih.gov/nuccore/ code 'NM_000059.3' = 'NM_000059.3', given
               as 'Homo sapiens BRCA2, DNA repair associated (BRCA2), mRNA'}) 

    <text> <status value="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"><p> <b> Generated Narrative</b> </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 &quot;breastcancer&quot; </p> </div> <p> <b> type</b> : rna</p> <p> <b> coordinateSystem</b> : 0</p> <p> <b> patient</b> : <a href="todo.html">Patient/brcapat</a> </p> <h3> ReferenceSeqs</h3> <table class="grid"><tr> <td> -</td> <td> <b> ReferenceSeqId</b> </td> <td> <b> WindowStart</b> </td> <td> <b> WindowEnd</b> </td> </tr> <tr> <td> *</td> <td> Homo sapiens BRCA2, DNA repair associated (BRCA2), mRNA <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (#NM_000059.3)</span> </td> <td> 101488058</td> <td> 101499444</td> </tr> </table> <h3> Variants</h3> <table class="grid"><tr> <td> -</td> <td> <b> Start</b> </td> <td> <b> End</b> </td> <td> <b> ObservedAllele</b> </td> <td> <b> ReferenceAllele</b> </td> </tr> <tr> <td> *</td> <td> 32316186</td> <td> 32316187</td> <td> A</td> <td> C</td> </tr> </table> </div> </text> <type value="rna"/>  

  <coordinateSystem value="0"/> 
  <patient> 
        

        <reference value="Patient/brcapat"/> 
    </patient> 
  <referenceSeq> 
        <referenceSeqId> 
            <coding> 
                <system value="http://www.ncbi.nlm.nih.gov/nuccore/"/> 
                <code value="NM_000059.3"/> 
                <display value="Homo sapiens BRCA2, DNA repair associated (BRCA2), mRNA"/> 
            </coding> 
        </referenceSeqId> 
    <windowStart value="101488058"/> 
    <windowEnd value="101499444"/> 
    </referenceSeq>       
    <variant> 
    <start value="32316186"/> 
    <end value="32316187"/> 
    <observedAllele value="A"/> 
    <referenceAllele value="C"/> 
  </variant> 


</

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.