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Example MolecularSequence/sequence-example-fusion (XML)

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

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

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BCR-ABL1 fusion (COSMIC https://cancer.sanger.ac.uk/cosmic/fusion/summary?id=1755). 5-prime end comprised of BCR exons 1-14. 3-prime end comprised of ABL1 exons 2-11. (id = "sequence-example-fusion")

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

<MolecularSequence xmlns="http://hl7.org/fhir">
    <!--    BCR-ABL1 fusion (COSMIC https://cancer.sanger.ac.uk/cosmic/fusion/summary?id=1755).
   5-prime end comprised of BCR exons 1-14. 3-prime end comprised of ABL1 exons 2-11.
      -->
    <id value="sequence-example-fusion"/> 
    <text> <status value="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"><p> <b> Generated Narrative: MolecularSequence</b> <a name="sequence-example-fusion"> </a> </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 MolecularSequence &quot;sequence-example-fusion&quot; </p> </div> <p> <b> type</b> : rna</p> <blockquote> <p> <b> relative</b> </p> <p> <b> coordinateSystem</b> : 1-based character counting <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a> #LA30102-0)</span> </p> <p> <b> ordinalPosition</b> : 1</p> <p> <b> sequenceRange</b> : 1-3234</p> <h3> StartingSequences</h3> <table class="grid"><tr> <td> -</td> <td> <b> Sequence[x]</b> </td> <td> <b> WindowStart</b> </td> <td> <b> WindowEnd</b> </td> </tr> <tr> <td> *</td> <td> NM_004327.4 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (nuccore#NM_004327.4)</span> </td> <td> 1</td> <td> 3234</td> </tr> </table> </blockquote> <blockquote> <p> <b> relative</b> </p> <p> <b> coordinateSystem</b> : 1-based character counting <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a> #LA30102-0)</span> </p> <p> <b> ordinalPosition</b> : 2</p> <p> <b> sequenceRange</b> : 3235-8367</p> <h3> StartingSequences</h3> <table class="grid"><tr> <td> -</td> <td> <b> Sequence[x]</b> </td> <td> <b> WindowStart</b> </td> <td> <b> WindowEnd</b> </td> </tr> <tr> <td> *</td> <td> NM_005157.6 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (nuccore#NM_005157.6)</span> </td> <td> 174</td> <td> 5306</td> </tr> </table> </blockquote> </div> </text> <type value="rna"/> 
    <relative> 
        <coordinateSystem> 
            <coding> 
                <system value="http://loinc.org"/> 
                <code value="LA30102-0"/> 
                <display value="1-based character counting"/> 
            </coding> 
        </coordinateSystem> 
        <ordinalPosition value="1"/> 
        <sequenceRange> 
            <low> 
                <value value="1"/> 
            </low> 
            <high> 
                <value value="3234"/> 
            </high> 
        </sequenceRange> 
        <startingSequence> 
            <sequenceCodeableConcept> 
                <coding> 
                    <system value="http://www.ncbi.nlm.nih.gov/nuccore"/> 
                    <code value="NM_004327.4"/> 
                </coding> 
            </sequenceCodeableConcept> 
            <windowStart value="1"/> 
            <windowEnd value="3234"/> 
        </startingSequence> 
    </relative> 
    <relative> 
        <coordinateSystem> 
            <coding> 
                <system value="http://loinc.org"/> 
                <code value="LA30102-0"/> 
                <display value="1-based character counting"/> 
            </coding> 
        </coordinateSystem> 
        <ordinalPosition value="2"/> 
        <sequenceRange> 
            <low> 
                <value value="3235"/> 
            </low> 
            <high> 
                <value value="8367"/> 
            </high> 
        </sequenceRange> 
        <startingSequence> 
            <sequenceCodeableConcept> 
                <coding> 
                    <system value="http://www.ncbi.nlm.nih.gov/nuccore"/> 
                    <code value="NM_005157.6"/> 
                </coding> 
            </sequenceCodeableConcept> 
            <windowStart value="174"/> 
            <windowEnd value="5306"/> 
        </startingSequence> 
    </relative> 
</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.