This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

• Narrative Content
• XML
• JSON
• TTL

: Example - Observation-Pgx-var-1019 - XML Representation

Raw xml | Download

<Observation xmlns="http://hl7.org/fhir">
  <id value="Pgx-var-1019"/>
  <meta>
    <profile
             value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
  </meta>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><p></p><p><b>category</b>: <span title="Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</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="Patient-CGPatientExample01.html">Generated Summary: Medical Record Number: m123 (USUAL); Adam B. Everyman ; gender: male; birthDate: 1951-01-20</a></p><p><b>effective</b>: 2020-01-01</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 81290-9}">Genomic DNA change (gHGVS)</span></p><p><b>value</b>: <span title="Codes: {http://varnomen.hgvs.org NC_000016.9:g.31096368C&gt;T}">NC_000016.9:g.31096368C&gt;T</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes: {http://loinc.org 48002-0}">Genomic source class [Type]</span></p><p><b>value</b>: <span title="Codes: {http://loinc.org LA6683-2}">Germline</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 48018-6}">Gene studied [ID]</span></p><p><b>value</b>: <span title="Codes: {http://www.genenames.org/geneId HGNC:23663}">VKORC1</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes: {http://loinc.org 48019-4}">DNA Change Type</span></p><p><b>value</b>: <span title="Codes: {http://sequenceontology.org SO:1000002}">substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes: {http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: &gt;20</p></blockquote></div>
  </text>
  <status value="final"/>
  <category>
    <coding>
      <system value="http://terminology.hl7.org/CodeSystem/observation-category"/>
      <code value="laboratory"/>
    </coding>
  </category>
  <code>
    <coding>
      <system value="http://loinc.org"/>
      <code value="69548-6"/>
    </coding>
  </code>
  <subject>
    <reference value="Patient/CGPatientExample01"/>
  </subject>
  <effectiveDateTime value="2020-01-01"/>
  <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="81290-9"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://varnomen.hgvs.org"/>
        <code value="NC_000016.9:g.31096368C&gt;T"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48002-0"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA6683-2"/>
        <display value="Germline"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="53034-5"/>
      </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="48018-6"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://www.genenames.org/geneId"/>
        <code value="HGNC:23663"/>
        <display value="VKORC1"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48019-4"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://sequenceontology.org"/>
        <code value="SO:1000002"/>
        <display value="substitution"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="82121-5"/>
      </coding>
    </code>
    <valueQuantity>
      <value value="20"/>
      <comparator value="&gt;"/>
    </valueQuantity>
  </component>
</Observation>