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

## : RepeatExpansion - XML Representation

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    <Observation xmlns="http://hl7.org/fhir">
      <id value="RepeatExpansion"/>
      <meta>
        <profile
                 value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
      </meta>
      <text>
        <status value="extensions"/>
        <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: Observation RepeatExpansion</b></p><a name="RepeatExpansion"> </a><a name="hcRepeatExpansion"> </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><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:8565}">PABPN1</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:">chr14</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_004643.4}">NM_004643.4</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_004643.3:c.3GGC[14]}">NM_004643.3:c.3GGC[14]</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81254-5}">Genomic allele start-end</span></p><p><b>value</b>: 3-?</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81252-9}">Discrete genetic variant</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/clinvar 503634}">NM_004643.3(PABPN1):c.3GGC[11] (p.Ala11_Gly12insAlaAlaAlaAla)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 1</p><p><b>code</b>: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-motif}">Repeat Expansion Motif</span></p><p><b>value</b>: GGC</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 1</p><p><b>code</b>: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-number}">Number of Repeat Expansions</span></p><p><b>value</b>: 11</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>
      <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:8565"/>
            <display value="PABPN1"/>
          </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="chr14"/>
        </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_004643.4"/>
            <display value="NM_004643.4"/>
          </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_004643.3:c.3GGC[14]"/>
            <display value="NM_004643.3:c.3GGC[14]"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="81254-5"/>
            <display value="Genomic allele start-end"/>
          </coding>
        </code>
        <valueRange>
          <low>
            <value value="3"/>
          </low>
        </valueRange>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="81252-9"/>
            <display value="Discrete genetic variant"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://www.ncbi.nlm.nih.gov/clinvar"/>
            <code value="503634"/>
            <display
                     value="NM_004643.3(PABPN1):c.3GGC[11] (p.Ala11_Gly12insAlaAlaAlaAla)"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <extension
                   url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order">
          <valuePositiveInt value="1"/>
        </extension>
        <code>
          <coding>
            <system
                    value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
            <code value="repeat-motif"/>
            <display value="Repeat Expansion Motif"/>
          </coding>
        </code>
        <valueString value="GGC"/>
      </component>
      <component>
        <extension
                   url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order">
          <valuePositiveInt value="1"/>
        </extension>
        <code>
          <coding>
            <system
                    value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
            <code value="repeat-number"/>
            <display value="Number of Repeat Expansions"/>
          </coding>
        </code>
        <valueQuantity>
          <value value="11"/>
        </valueQuantity>
      </component>
    </Observation>