Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

: Pgx-var-1015 - XML Representation

Raw xml | Download



<Observation xmlns="http://hl7.org/fhir">
  <id value="Pgx-var-1015"/>
  <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: Observation</b><a name="Pgx-var-1015"> </a><a name="hcPgx-var-1015"> </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 Observation &quot;Pgx-var-1015&quot; </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-variant.html">Variant</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-observation-category.html">Observation Category Codes</a>#laboratory)</span>, Genetics <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Genetic var assess <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69548-6)</span></p><p><b>subject</b>: <a href="Patient-CGPatientExample01.html">Patient/CGPatientExample01</a> &quot; EVERYMAN&quot;</p><p><b>effective</b>: 2019-04-01</p><p><b>performer</b>: <a href="Organization-ExampleOrg.html">Organization/ExampleOrg</a> &quot;some lab&quot;</p><p><b>value</b>: Present <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA9633-4)</span></p><p><b>method</b>: Sequencing <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA26398-0)</span></p><blockquote><p><b>component</b></p><p><b>code</b>: Struct var HGVS name <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81290-9)</span></p><p><b>value</b>: NC_000010.10:g.96540410G&gt;A <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html">Human Genome Variation Society nomenclature</a>#NC_000010.10:g.96540410G&gt;A)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48002-0)</span></p><p><b>value</b>: Germline <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA6683-2)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic state <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#53034-5)</span></p><p><b>value</b>: homozygous <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA6705-3)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied ID <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48018-6)</span></p><p><b>value</b>: CYP2C19 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgnc.html">HUGO Gene Nomenclature Committee Genes</a>#HGNC:2621)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA Change Type <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48019-4)</span></p><p><b>value</b>: substitution <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (sequenceontology.org#SO:1000002)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic read depth <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#82121-5)</span></p><p><b>value</b>: &gt;20</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Variant Confidence Status <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#variant-confidence-status)</span></p><p><b>value</b>: High <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-variant-confidence-status-cs.html">Variant Confidence Status Codes</a>#high)</span></p></blockquote></div>
  </text>
  <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"/>
    </coding>
  </code>
  <subject>🔗 
    <reference value="Patient/CGPatientExample01"/>
  </subject>
  <effectiveDateTime value="2019-04-01"/>
  <performer>🔗 
    <reference value="Organization/ExampleOrg"/>
  </performer>
  <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_000010.10:g.96540410G&gt;A"/>
      </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="LA6705-3"/>
        <display value="homozygous"/>
      </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"/>
        <code value="HGNC:2621"/>
        <display value="CYP2C19"/>
      </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>
  <component>
    <code>
      <coding>
        <system
                value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
        <code value="variant-confidence-status"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system
                value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/variant-confidence-status-cs"/>
        <code value="high"/>
      </coding>
    </valueCodeableConcept>
  </component>
</Observation>