Sequence-example-pgx-1.xml

Example of a single varaint on a reference MolecularSequence related to a haplotype observation in PGx example (id = "example-pgx-1")

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

<MolecularSequence xmlns="http://hl7.org/fhir">
    <id value="example-pgx-1"/> 
    <text> <status value="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"><p> <b> Generated Narrative</b> </p> <p> <b> id</b> : example-pgx-1</p> <p> <b> type</b> : dna</p> <p> <b> coordinateSystem</b> : 0</p> <p> <b> patient</b> : <a> Generated Summary: id: example; Medical record number: 12345 (USUAL); active; Peter James
           Chalmers (OFFICIAL), Jim , Peter James Windsor (MAIDEN); -unknown-(HOME), ph: (03) 5555
           6473(WORK), ph: (03) 3410 5613(MOBILE), ph: (03) 5555 8834(OLD); gender: male; birthDate:
           1974-12-25; </a> </p> <h3> ReferenceSeqs</h3> <table> <tr> <td> -</td> <td> <b> Orientation</b> </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> sense</td> <td> <span> NG_007726.3</span> </td> <td> watson</td> <td> 55227970</td> <td> 55227980</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> VariantPointer</b> </td> </tr> <tr> <td> *</td> <td> 55227976</td> <td> 55227977</td> <td> G</td> <td> T</td> <td> <a> Target Haplotype Observation</a> </td> </tr> </table> </div> </text> <type value="dna"/> 
    <coordinateSystem value="0"/> 
    <patient> 
        <reference value="Patient/example"/> 
    </patient> 
    <referenceSeq> 
        <orientation value="sense"/> 
        <referenceSeqId> 
          <coding> 
            <system value="http://www.ncbi.nlm.nih.gov/nuccore"/> 
            <code value="NG_007726.3"/> 
          </coding> 
        </referenceSeqId> 
        <strand value="watson"/> 
        <windowStart value="55227970"/> 
        <windowEnd value="55227980"/> 
    </referenceSeq> 
    <variant> 
        <start value="55227976"/> 
        <end value="55227977"/> 
        <observedAllele value="G"/> 
        <referenceAllele value="T"/> 
        <variantPointer> 
          <reference value="Observation/example-haplotype1"/> 
          <display value="Target Haplotype Observation"/> 
        </variantPointer> 
    </variant> 
</MolecularSequence>