Genomics Reporting Implementation Guide
3.0.0 - STU3 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 3.0.0 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

: ExampleGermlineCNV - XML Representation

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<Observation xmlns="http://hl7.org/fhir">
  <id value="ExampleGermlineCNV"/>
  <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 ExampleGermlineCNV</b></p><a name="ExampleGermlineCNV"> </a><a name="hcExampleGermlineCNV"> </a><a name="ExampleGermlineCNV-en-US"> </a><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-CGPatientExample01.html">Adam B. Everyman  Male, DoB: 1951-01-20 ( Medical Record Number: m123 (use: usual, ))</a></p><p><b>effective</b>: 2019-04-01</p><p><b>performer</b>: <a href="Organization-ExampleOrg.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><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://www.sequenceontology.org SO:0001019}">copy_number_variation</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</span></p><p><b>value</b>: T</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 48013-7}">Genomic reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NC_000022.10}">NC_000022.10</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82155-3}">Genomic structural variant copy number</span></p><p><b>value</b>: 3 1<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 92822-6}">Genomic coordinate system [Type]</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA30102-0}">1-based character counting</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81302-2}">Structural variant inner start and end</span></p><p><b>value</b>: 42523949-42533891</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 94186-4}">Origin of germline genetic variant [Type]</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA26320-4}">Maternal</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82309-6}">Basis for allelic phase [Type]</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA26426-9}">Directly measured</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="48019-4"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://www.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="LA6683-2"/>
        <display value="Germline"/>
      </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/refseq"/>
        <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>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="94186-4"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA26320-4"/>
        <display value="Maternal"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="82309-6"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA26426-9"/>
        <display value="Directly measured"/>
      </coding>
    </valueCodeableConcept>
  </component>
</Observation>