Release 4 5 Snapshot #1

This page is part of the FHIR Specification (v4.0.1: R4 - Mixed Normative and STU ) in it's permanent home (it will always be available at this URL). (v5.0.0-snapshot1: Release 5 Snapshot #1). The current version which supercedes this version is 5.0.0 . For a full list of available versions, see the Directory of published versions . Page versions: R5 R4B R4 R3

Sequence-example-pgx-1.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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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> <div> <p> Resource &quot;example-pgx-1&quot; </p> </div> <p> <b> type</b> : dna</p> <p> <b> coordinateSystem</b> : 0</p> <p> <b> patient</b> : <a> Patient/example</a>  &quot;Peter CHALMERS&quot;</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> NG_007726.3 <span>  (nuccore#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> Observation/example-haplotype1: 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

>

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.