Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild 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

## : SNVexample - XML Representation

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    <Observation xmlns="http://hl7.org/fhir">
      <id value="SNVexample"/>
      <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 class="res-header-id"><b>Generated Narrative: Observation SNVexample</b></p><a name="SNVexample"> </a><a name="hcSNVexample"> </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-variant.html">Variant</a></p></div><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="Patient-ExamplePatient.html">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2023-06-01</p><p><b>performer</b>: <a href="Organization-ExampleLab.html">Organization Some lab</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><p><b>specimen</b>: Identifier: <code>http://slk-kliniken.de/fhir/namingSystem/tissueID</code>/16-123456-23</p><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 HGNC:644}">AR</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48001-2}">Cytogenetic (chromosome) location</span></p><p><b>value</b>: <span title="Codes:">chrX</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_000044.6:c.7G&gt;A}">NM_000044.6:c.7G&gt;A</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48005-3}">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NP_000035.2:p.Val3Met}">NP_000035.2:p.Val3Met</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_000044.3}">NM_000044.6</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.44 decimal</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>: 120 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</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"/>
          <display value="Genetic variant assessment"/>
        </coding>
      </code>
      <subject>🔗
        <reference value="Patient/ExamplePatient"/>
      </subject>
      <effectiveDateTime value="2023-06-01"/>
      <performer>🔗
        <reference value="Organization/ExampleLab"/>
      </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>
      <specimen>
        <identifier>
          <system value="http://slk-kliniken.de/fhir/namingSystem/tissueID"/>
          <value value="16-123456-23"/>
        </identifier>
      </specimen>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="48018-6"/>
            <display value="Gene studied ID"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://www.genenames.org"/>
            <code value="HGNC:644"/>
            <display value="AR"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="48001-2"/>
            <display value="Cytogenetic (chromosome) location"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <text value="chrX"/>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="62374-4"/>
            <display value="Human reference sequence assembly version"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA14029-5"/>
            <display value="GRCh37"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="48002-0"/>
            <display value="Genomic source class"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA6684-0"/>
            <display value="Somatic"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="48004-6"/>
            <display value="DNA change (c.HGVS)"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://varnomen.hgvs.org"/>
            <code value="NM_000044.6:c.7G&gt;A"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="48005-3"/>
            <display value="Amino acid change (pHGVS)"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://varnomen.hgvs.org"/>
            <code value="NP_000035.2:p.Val3Met"/>
            <display value="NP_000035.2:p.Val3Met"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="51958-7"/>
            <display value="Transcript reference sequence [ID]"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
            <code value="NM_000044.3"/>
            <display value="NM_000044.6"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="81258-6"/>
            <display value="Sample VAF"/>
          </coding>
        </code>
        <valueQuantity>
          <value value="0.44"/>
          <unit value="decimal"/>
          <system value="http://unitsofmeasure.org"/>
        </valueQuantity>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="82121-5"/>
            <display value="Allelic read depth"/>
          </coding>
        </code>
        <valueQuantity>
          <value value="120"/>
          <unit value="reads per base pair"/>
          <system value="http://unitsofmeasure.org"/>
          <code value="1"/>
        </valueQuantity>
      </component>
    </Observation>