Genomics Reporting Implementation Guide
2.0.0 - trial-use

This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

: ExampleSomaticCNV - XML Representation

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<Observation xmlns="http://hl7.org/fhir">
  <id value="ExampleSomaticCNV"/>
  <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><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 "ExampleSomaticCNV" </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/3.1.0/CodeSystem-observation-category.html">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Genetic variant assessment <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> " EVERYMAN"</p><p><b>effective</b>: 2019-04-01</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>: 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>: copy_number_variation <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (sequenceontology.org#SO:0001019)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic ref allele [ID] <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69547-8)</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class [Type] <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>: Somatic <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA6684-0)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic reference sequence [ID] <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48013-7)</span></p><p><b>value</b>: NC_000022.10 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (nuccore#NC_000022.10)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic structural variant copy number <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#82155-3)</span></p><p><b>value</b>: 3 1<span style="background: LightGoldenRodYellow"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic coordinate system [Type] <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#92822-6)</span></p><p><b>value</b>: 1-based character counting <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA30102-0)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Structural variant inner start and end <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81302-2)</span></p><p><b>value</b>: 42523949-42533891</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="2019-04-01"/>
  <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="48019-4"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://sequenceontology.org"/>
        <code value="SO:0001019"/>
        <display value="copy_number_variation"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="69547-8"/>
      </coding>
    </code>
    <valueString value="T"/>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48002-0"/>
      </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="48013-7"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://www.ncbi.nlm.nih.gov/nuccore"/>
        <code value="NC_000022.10"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="82155-3"/>
      </coding>
    </code>
    <valueQuantity>
      <value value="3"/>
      <system value="http://unitsofmeasure.org"/>
      <code value="1"/>
    </valueQuantity>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="92822-6"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA30102-0"/>
        <display value="1-based character counting"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="81302-2"/>
      </coding>
    </code>
    <valueRange>
      <low>
        <value value="42523949"/>
      </low>
      <high>
        <value value="42533891"/>
      </high>
    </valueRange>
  </component>
</Observation>