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="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: Observation MultipleRepeatExpansions</b></p><a name="MultipleRepeatExpansions"> </a><a name="hcMultipleRepeatExpansions"> </a><a name="hcMultipleRepeatExpansions-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-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:3775}">FMR1</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 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_002024.5}">NM_002024.5</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_002024.5:c.-128_-69GGC[10]GGA[1]GGC[9]GGA[1]GGC[10]}">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>: <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://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>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>: 10</p></blockquote><blockquote><p><b>component</b></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>: GGA</p></blockquote><blockquote><p><b>component</b></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>: 1</p></blockquote><blockquote><p><b>component</b></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>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>: 9</p></blockquote><blockquote><p><b>component</b></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>: GGA</p></blockquote><blockquote><p><b>component</b></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>: 1</p></blockquote><blockquote><p><b>component</b></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>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>: 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>