This page is part of the Genetic Reporting Implementation Guide (v1.0.0: STU 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

Example - NGS - XML Representation

(back to narrative)

Raw xml

<!-- query1: Observation?code-value-concept=http://loinc.org|69548-6$http://loinc.org|LA9633-4  -->
<!-- query2: Observation?component-code-value-concept=http://loinc.org|48018-6$https://www.genenames.org|HGNC:644  -->
<!-- query3: Observation?component-code-value-concept=http://loinc.org|48002-0$http://loinc.org|LA6684-0  -->
<!-- query4: Observation?component-code-value-concept=http://loinc.org|48006-1$http://varnomen.hgvs.org|p.(Ala412Val)  -->
<Observation xmlns="http://hl7.org/fhir">
  <id value="SNVexample"/>
  <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 with Details</b></p><p><b>id</b>: SNVexample</p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style="background: LightGoldenRodYellow">(Details : {LOINC code '69548-6' = 'Genetic variant assessment', given as 'Genetic variant assessment'})</span></p><p><b>value</b>: Present <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA9633-4' = 'Present', given as 'Present'})</span></p><p><b>method</b>: Sequencing <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA26398-0' = 'Sequencing', given as 'Sequencing'})</span></p><p><b>specimen</b>: </p><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied ID <span style="background: LightGoldenRodYellow">(Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'})</span></p><p><b>value</b>: AR <span style="background: LightGoldenRodYellow">(Details : {http://www.genenames.org/geneId code 'HGNC:644' = 'HGNC:644', given as 'AR'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Cytogenetic (chromosome) location <span style="background: LightGoldenRodYellow">(Details : {LOINC code '48001-2' = 'Cytogenetic (chromosome) location', given as 'Cytogenetic (chromosome) location'})</span></p><p><b>value</b>: chrX <span style="background: LightGoldenRodYellow">(Details )</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Human reference sequence assembly version <span style="background: LightGoldenRodYellow">(Details : {LOINC code '62374-4' = 'Human reference sequence assembly version', given as 'Human reference sequence assembly version'})</span></p><p><b>value</b>: GRCh37 <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA14029-5' = 'GRCh37', given as 'GRCh37'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class <span style="background: LightGoldenRodYellow">(Details : {LOINC code '48002-0' = 'Genomic source class [Type]', given as 'Genomic source class'})</span></p><p><b>value</b>: Somatic <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA6684-0' = 'Somatic', given as 'Somatic'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change (pHGVS) <span style="background: LightGoldenRodYellow">(Details : {LOINC code '48005-3' = 'Amino acid change (pHGVS)', given as 'Amino acid change (pHGVS)'})</span></p><p><b>value</b>: p.(Ala412Val) <span style="background: LightGoldenRodYellow">(Details : {http://varnomen.hgvs.org code 'p.(Ala412Val)' = 'p.(Ala412Val)', given as 'p.(Ala412Val)'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change type <span style="background: LightGoldenRodYellow">(Details : {LOINC code '48006-1' = 'Amino acid change [Type]', given as 'Amino acid change type'})</span></p><p><b>value</b>: Missense <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA6698-0' = 'Missense', given as 'Missense'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style="background: LightGoldenRodYellow">(Details : {LOINC code '51958-7' = 'Transcript reference sequence [ID]', given as 'Transcript reference sequence [ID]'})</span></p><p><b>value</b>: NM_000044.3 <span style="background: LightGoldenRodYellow">(Details : {http://www.ncbi.nlm.nih.gov/refseq code 'NM_000044.3' = 'NM_000044.3', given as 'NM_000044.3'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample variant allelic frequency [NFr] <span style="background: LightGoldenRodYellow">(Details : {LOINC code '81258-6' = 'Sample variant allelic frequency [NFr]', given as 'Sample variant allelic frequency [NFr]'})</span></p><p><b>value</b>: 0.44 decimal</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic read depth <span style="background: LightGoldenRodYellow">(Details : {LOINC code '82121-5' = 'Allelic read depth', given as 'Allelic read depth'})</span></p><p><b>value</b>: 120 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM code {reads}/{base} = '{reads}/{base}')</span></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"/>
      <display value="Genetic variant assessment"/>
    </coding>
  </code>
<!-- 
  <subject>
    <reference value="Patient/12345" />
  </subject>

  <performer>
    <reference value="Organization/CeGaT"/>
  </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>
  <specimen>
    <identifier>
      <system value="http://slk-kliniken.de/fhir/namingSystem/tissueID"/>
      <value value="16-123456-23"/>
    </identifier>
  </specimen>
  <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/geneId"/>
        <code value="HGNC:644"/>
        <display value="AR"/>
      </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="62374-4"/>
        <display value="Human reference sequence assembly version"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA14029-5"/>
        <display value="GRCh37"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48002-0"/>
        <display value="Genomic source class"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA6684-0"/>
      <!--  fine  -->
        <display value="Somatic"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48005-3"/>
        <display value="Amino acid change (pHGVS)"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://varnomen.hgvs.org"/>
        <code value="p.(Ala412Val)"/>
        <display value="p.(Ala412Val)"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48006-1"/>
        <display value="Amino acid change type"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA6698-0"/>
        <display value="Missense"/>
      </coding>
    </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_000044.3"/>
        <display value="NM_000044.3"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="81258-6"/>
        <display value="Sample variant allelic frequency [NFr]"/>
      </coding>
    </code>
    <valueQuantity>
      <value value="0.44"/>
      <unit value="decimal"/>
      <system value="http://unitsofmeasure.org"/>
    </valueQuantity>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="82121-5"/>
        <display value="Allelic read depth"/>
      </coding>
    </code>
    <valueQuantity>
      <value value="120"/>
      <unit value="reads per base pair"/>
      <system value="http://unitsofmeasure.org"/>
      <code value="{reads}/{base}"/>
    </valueQuantity>
  </component>
</Observation>