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: Genomic Report BRCA1 Variant Example - XML Representation

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<Observation xmlns="http://hl7.org/fhir">
  <id value="brca1-variant"/>
  <meta>
    <profile
             value="https://nw-gmsa.github.io/StructureDefinition/Observation-Variant"/>
  </meta>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: Observation brca1-variant</b></p><a name="brca1-variant"> </a><a name="hcbrca1-variant"> </a><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"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-Observation-Variant.html">Observation Variant</a></p></div><p><b>identifier</b>: <a href="http://terminology.hl7.org/6.2.0/NamingSystem-uri.html" title="As defined by RFC 3986 (http://www.ietf.org/rfc/rfc3986.txt)(with many schemes defined in many RFCs). For OIDs and UUIDs, use the URN form (urn:oid:(note: lowercase) and urn:uuid:). See http://www.ietf.org/rfc/rfc3001.txt and http://www.ietf.org/rfc/rfc4122.txt 

This oid is used as an identifier II.root to indicate the the extension is an absolute URI (technically, an IRI). Typically, this is used for OIDs and GUIDs. Note that when this OID is used with OIDs and GUIDs, the II.extension should start with urn:oid or urn:uuid: 

Note that this OID is created to aid with interconversion between CDA and FHIR - FHIR uses urn:ietf:rfc:3986 as equivalent to this OID. URIs as identifiers appear more commonly in FHIR.

This OID may also be used in CD.codeSystem.">Uniform Resource Identifier (URI)</a>/urn:uuid:dfa620b9-0b78-4c57-8f20-7772131b917d</p><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>subject</b>: <a href="Bundle-FHIRDocumentGeneticReportBundle.html#urn-uuid-d6faafcf-db64-4c11-9da8-25f36774c1bd">Octavia CHISLETT</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48013-7}">Genomic reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.genenames.org HGNC:1100}">BRCA1</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 53034-5}">Allelic state</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6706-1}">Heterozygous</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org BRCA1:c.3143delG p.(Gly1048ValfsTer14)}">BRCA1:c.3143delG p.(Gly1048ValfsTer14)</span></p></blockquote></div>
  </text>
  <identifier>
    <system value="urn:ietf:rfc:3986"/>
    <value value="urn:uuid:dfa620b9-0b78-4c57-8f20-7772131b917d"/>
  </identifier>
  <status value="final"/>
  <category>
    <coding>
      <system
              value="http://terminology.hl7.org/CodeSystem/observation-category"/>
      <code value="laboratory"/>
    </coding>
  </category>
  <category>
    <coding>
      <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
      <code value="GE"/>
    </coding>
  </category>
  <code>
    <coding>
      <system value="http://loinc.org"/>
      <code value="69548-6"/>
      <display value="Genetic variant assessment"/>
    </coding>
  </code>
  <subject>
    <reference value="urn:uuid:d6faafcf-db64-4c11-9da8-25f36774c1bd"/>
    <identifier>
      <system value="https://fhir.nhs.uk/Id/nhs-number"/>
      <value value="9449305552"/>
    </identifier>
    <display value="Octavia CHISLETT"/>
  </subject>
  <valueCodeableConcept>
    <coding>
      <system value="http://loinc.org"/>
      <code value="LA9633-4"/>
      <display value="Present"/>
    </coding>
  </valueCodeableConcept>
  <method>
    <coding>
      <system value="http://loinc.org"/>
      <code value="LA26398-0"/>
      <display value="Sequencing"/>
    </coding>
  </method>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48013-7"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://www.genenames.org"/>
        <code value="HGNC:1100"/>
        <display value="BRCA1"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="53034-5"/>
        <display value="Allelic state"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA6706-1"/>
        <display value="Heterozygous"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48004-6"/>
        <display value="DNA change"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://varnomen.hgvs.org"/>
        <code value="BRCA1:c.3143delG p.(Gly1048ValfsTer14)"/>
      </coding>
    </valueCodeableConcept>
  </component>
</Observation>