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

: MultipleRepeatExpansions - XML Representation

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<Observation xmlns="http://hl7.org/fhir">
  <id value="MultipleRepeatExpansions"/>
  <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><b>Generated Narrative: Observation</b><a name="MultipleRepeatExpansions"> </a><a name="hcMultipleRepeatExpansions"> </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;MultipleRepeatExpansions&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 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-ExamplePatient.html">Patient/ExamplePatient</a></p><p><b>effective</b>: 2023-06-01</p><p><b>performer</b>: <a href="Organization-ExampleLab.html">Organization/ExampleLab</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><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>: FMR1 <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:3775)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Cytogenetic (chromosome) location <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48001-2)</span></p><p><b>value</b>: chrx <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> ()</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_002024.5 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-v3-refSeq.html">Gene Reference Sequence Collection</a>#NM_002024.5)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change (c.HGVS) <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48004-6)</span></p><p><b>value</b>: NM_002024.5:c.-128_-69GGC[10]GGA[1]GGC[9]GGA[1]GGC[10] <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>#NM_002024.5:c.-128_-69GGC[10]GGA[1]GGC[9]GGA[1]GGC[10])</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic allele start-end <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81254-5)</span></p><p><b>value</b>: 3-?</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 1</p><p><b>code</b>: Repeat Expansion Motif <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#repeat-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>: Number of Repeat Expansions <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#repeat-number)</span></p><p><b>value</b>: 10</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 2</p><p><b>code</b>: Repeat Expansion Motif <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#repeat-motif)</span></p><p><b>value</b>: GGA</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 2</p><p><b>code</b>: Number of Repeat Expansions <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#repeat-number)</span></p><p><b>value</b>: 1</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 3</p><p><b>code</b>: Repeat Expansion Motif <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#repeat-motif)</span></p><p><b>value</b>: GGC</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 3</p><p><b>code</b>: Number of Repeat Expansions <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#repeat-number)</span></p><p><b>value</b>: 9</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 4</p><p><b>code</b>: Repeat Expansion Motif <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#repeat-motif)</span></p><p><b>value</b>: GGA</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 4</p><p><b>code</b>: Number of Repeat Expansions <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#repeat-number)</span></p><p><b>value</b>: 1</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 5</p><p><b>code</b>: Repeat Expansion Motif <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#repeat-motif)</span></p><p><b>value</b>: GGC</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 5</p><p><b>code</b>: Number of Repeat Expansions <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#repeat-number)</span></p><p><b>value</b>: 10</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:3775"/>
        <display value="FMR1"/>
      </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="51958-7"/>
        <display value="Transcript reference sequence [ID]"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
        <code value="NM_002024.5"/>
        <display value="NM_002024.5"/>
      </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_002024.5:c.-128_-69GGC[10]GGA[1]GGC[9]GGA[1]GGC[10]"/>
        <display
                 value="NM_002024.5:c.-128_-69GGC[10]GGA[1]GGC[9]GGA[1]GGC[10]"/>
      </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>
    <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="10"/>
    </valueQuantity>
  </component>
  <component>
    <extension
               url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order">
      <valuePositiveInt value="2"/>
    </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="GGA"/>
  </component>
  <component>
    <extension
               url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order">
      <valuePositiveInt value="2"/>
    </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="1"/>
    </valueQuantity>
  </component>
  <component>
    <extension
               url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order">
      <valuePositiveInt value="3"/>
    </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="3"/>
    </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="9"/>
    </valueQuantity>
  </component>
  <component>
    <extension
               url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order">
      <valuePositiveInt value="4"/>
    </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="GGA"/>
  </component>
  <component>
    <extension
               url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order">
      <valuePositiveInt value="4"/>
    </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="1"/>
    </valueQuantity>
  </component>
  <component>
    <extension
               url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order">
      <valuePositiveInt value="5"/>
    </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="5"/>
    </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="10"/>
    </valueQuantity>
  </component>
</Observation>