Sequence-example.xml

Example of a patient with a EGFR mutation associated with lung cancer (id = "example")

<Sequence xmlns="http://hl7.org/fhir">
    <id value="example"/>
    <text><status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: example</p><p><b>type</b>: DNA</p><p><b>variationID</b>: rs587778247 <span>(Details : {http://www.ncbi.nlm.nih.gov/projects/SNP code '587778247' = '??)</span></p><p><b>referenceSeq</b>: ENSESTT00000085772.1 <span>(Details : {http://www.ensembl.org code 'ENSESTT00000085772.1' = '??)</span></p><h3>Coordinates</h3><table><tr><td>-</td><td><b>Chromosome</b></td><td><b>Start</b></td><td><b>End</b></td><td><b>GenomeBuild</b></td></tr><tr><td>*</td><td>7 <span>(Details )</span></td><td>55227976</td><td>55227977</td><td>GRCh37 <span>(Details )</span></td></tr></table><p><b>species</b>: Homo sapiens <span>(Details : {SNOMED CT code '337915000' = '??)</span></p><p><b>observedAllele</b>: T</p><p><b>referenceAllele</b>: A</p><h3>Repositories</h3><table><tr><td>-</td><td><b>Url</b></td><td><b>Name</b></td><td><b>VariantId</b></td><td><b>ReadGroupSetId</b></td></tr><tr><td>*</td><td><a>https://www.googleapis.com/genomics/v1beta2</a></td><td>ga4gh</td><td>A1A2</td><td>B1B2</td></tr></table></div></text><type value="DNA"/>
    <variationID>
        <coding>
            <system value="http://www.ncbi.nlm.nih.gov/projects/SNP"/>
            <code value="587778247"/>
        </coding>
        <text value="rs587778247"/>
    </variationID>
    <referenceSeq>
        <coding>
            <system value="http://www.ensembl.org"/>
            <code value="ENSESTT00000085772.1"/>
        </coding>
        <text value="ENSESTT00000085772.1"/>
    </referenceSeq>
    <coordinate>
        <chromosome>
            <text value="7"/>
        </chromosome>
        <start value="55227976"/>
        <end value="55227977"/>
        <genomeBuild>
            <text value="GRCh37"/>
        </genomeBuild>
    </coordinate>
    <species>
        <coding>
            <system value="http://snomed.info/sct"/>
            <code value="337915000"/>
        </coding>
        <text value="Homo sapiens"/>
    </species>
    <observedAllele value="T"/>
    <referenceAllele value="A"/>
    <repository>
        <url value="https://www.googleapis.com/genomics/v1beta2"/>
        <name value="ga4gh"/>
        <variantId value="A1A2"/>
        <readGroupSetId value="B1B2"/>
    </repository>
</Sequence>