Release 4


Clinical Genomics Work GroupMaturity Level: N/AStandards Status: InformativeCompartments: 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="">
    <id value="breastcancer"/> 
    <text> <status value="generated"/> <div xmlns=""><p> <b> Generated Narrative with Details</b> </p> <p> <b> id</b> : breastcancer</p> <p> <b> type</b> : rna</p> <p> <b> coordinateSystem</b> : 0</p> <p> <b> patient</b> : <a> Patient/brcapat</a> </p> <h3> ReferenceSeqs</h3> <table> <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> (Details : { code 'NM_000059.3' = 'NM_000059.3', given
               as 'Homo sapiens BRCA2, DNA repair associated (BRCA2), mRNA'})</span> </td> <td> 101488058</td> <td> 101499444</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> </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"/> 
        <reference value="Patient/brcapat"/> 
                <system value=""/> 
                <code value="NM_000059.3"/> 
                <display value="Homo sapiens BRCA2, DNA repair associated (BRCA2), mRNA"/> 
    <windowStart value="101488058"/> 
    <windowEnd value="101499444"/> 
    <start value="32316186"/> 
    <end value="32316187"/> 
    <observedAllele value="A"/> 
    <referenceAllele value="C"/> 

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.