Genomics Reporting Implementation Guide
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This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

: lungMass-analysis1 - XML Representation

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<Procedure xmlns="http://hl7.org/fhir">
  <id value="lungMass-analysis1"/>
  <meta>
    <profile
             value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis"/>
  </meta>
  <text>
    <status value="extensions"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative: Procedure</b><a name="lungMass-analysis1"> </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 Procedure &quot;lungMass-analysis1&quot; </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-genomic-study-analysis.html">Genomic Study Analysis</a></p></div><p><b>Genomic Study Analysis Method Type</b>: Sequence analysis of the entire coding region <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-genomic-study-method-type-cs.html">Genomic Study Method Type CodeSystem</a>#sequence-analysis-of-the-entire-coding-region)</span></p><p><b>Genomic Study Analysis Change Type</b>: SNV <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (sequenceontology.org#SO:0001483)</span></p><p><b>Genomic Study Analysis Change Type</b>: MNV <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (sequenceontology.org#SO:0002007)</span></p><p><b>Genomic Study Analysis Change Type</b>: delins <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (sequenceontology.org#SO:1000032)</span></p><p><b>Genomic Study Analysis Genome Build</b>: GRCh38 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA26806-2)</span></p><p><b>Genomic Study Analysis Specimen</b>: <a href="Specimen-genomicSpecimen.html">Specimen/genomicSpecimen</a></p><p><b>Genomic Study Analysis Focus</b>: <a href="Patient-genomicPatient.html">Patient/genomicPatient</a> &quot; DOE&quot;</p><blockquote><p><b>Genomic Study Analysis Device</b></p><blockquote><p><b>url</b></p><code>device</code></blockquote><p><b>value</b>: <a href="Device-triodenovo-software.html">Device/triodenovo-software</a></p></blockquote><blockquote><p><b>Genomic Study Analysis Regions</b></p><blockquote><p><b>url</b></p><code>studied</code></blockquote><p><b>value</b>: <a href="DocumentReference-WES-FullSequencedRegion-GRCh38.html">DocumentReference/WES-FullSequencedRegion-GRCh38</a></p><blockquote><p><b>url</b></p><code>uncalled</code></blockquote><p><b>value</b>: <a href="DocumentReference-UncallableRegions.html">DocumentReference/UncallableRegions</a></p><blockquote><p><b>url</b></p><code>called</code></blockquote><p><b>value</b>: <a href="DocumentReference-SimpleVariantAnalysis-called.html">DocumentReference/SimpleVariantAnalysis-called</a></p></blockquote><blockquote><p><b>Genomic Study Analysis Output</b></p><blockquote><p><b>url</b></p><code>type</code></blockquote><p><b>value</b>: VCF <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-genomic-study-data-format-cs.html">Genomic Study Data Format CodeSystem</a>#vcf)</span></p><blockquote><p><b>url</b></p><code>file</code></blockquote><p><b>value</b>: <a href="DocumentReference-genomicVCFfile-simple.html">DocumentReference/genomicVCFfile-simple</a></p></blockquote><p><b>instantiatesUri</b>: <a href="https://pubmed.ncbi.nlm.nih.gov/33927380/">https://pubmed.ncbi.nlm.nih.gov/33927380/</a></p><p><b>status</b>: completed</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></p><p><b>subject</b>: <a href="Patient-genomicPatient.html">Patient/genomicPatient</a> &quot; DOE&quot;</p><p><b>performed</b>: 2019-03-01 01:01:10-0600</p><h3>Performers</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Function</b></td><td><b>Actor</b></td></tr><tr><td style="display: none">*</td><td>Performer <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-v3-ParticipationType.html">ParticipationType</a>#PRF)</span></td><td><a href="Practitioner-practitioner02.html">Practitioner/practitioner02</a> &quot; DOEL&quot;</td></tr></table><p><b>note</b>: For technical reasons, PIK3CB was deemed uncallable using this method.</p></div>
  </text>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-method-type">
    <valueCodeableConcept>
      <coding>
        <system
                value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs"/>
        <code value="sequence-analysis-of-the-entire-coding-region"/>
        <display value="Sequence analysis of the entire coding region"/>
      </coding>
    </valueCodeableConcept>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type">
    <valueCodeableConcept>
      <coding>
        <system value="http://sequenceontology.org"/>
        <code value="SO:0001483"/>
        <display value="SNV"/>
      </coding>
    </valueCodeableConcept>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type">
    <valueCodeableConcept>
      <coding>
        <system value="http://sequenceontology.org"/>
        <code value="SO:0002007"/>
        <display value="MNV"/>
      </coding>
    </valueCodeableConcept>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type">
    <valueCodeableConcept>
      <coding>
        <system value="http://sequenceontology.org"/>
        <code value="SO:1000032"/>
        <display value="delins"/>
      </coding>
    </valueCodeableConcept>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genome-build">
    <valueCodeableConcept>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA26806-2"/>
        <display value="GRCh38"/>
      </coding>
    </valueCodeableConcept>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen">
    <valueReference>🔗 
      <reference value="Specimen/genomicSpecimen"/>
    </valueReference>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus">
    <valueReference>🔗 
      <reference value="Patient/genomicPatient"/>
    </valueReference>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device">
    <extension url="device">
      <valueReference>🔗 
        <reference value="Device/triodenovo-software"/>
      </valueReference>
    </extension>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions">
    <extension url="studied">
      <valueReference>🔗 
        <reference value="DocumentReference/WES-FullSequencedRegion-GRCh38"/>
      </valueReference>
    </extension>
    <extension url="uncalled">
      <valueReference>🔗 
        <reference value="DocumentReference/UncallableRegions"/>
      </valueReference>
    </extension>
    <extension url="called">
      <valueReference>🔗 
        <reference value="DocumentReference/SimpleVariantAnalysis-called"/>
      </valueReference>
    </extension>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-output">
    <extension url="type">
      <valueCodeableConcept>
        <coding>
          <system
                  value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs"/>
          <code value="vcf"/>
          <display value="VCF"/>
        </coding>
      </valueCodeableConcept>
    </extension>
    <extension url="file">
      <valueReference>🔗 
        <reference value="DocumentReference/genomicVCFfile-simple"/>
      </valueReference>
    </extension>
  </extension>
  <instantiatesUri value="https://pubmed.ncbi.nlm.nih.gov/33927380/"/>
  <status value="completed"/>
  <category>
    <coding>
      <system
              value="http://terminology.hl7.org/CodeSystem/observation-category"/>
      <code value="laboratory"/>
    </coding>
  </category>
  <subject>🔗 
    <reference value="Patient/genomicPatient"/>
  </subject>
  <performedDateTime value="2019-03-01T01:01:10-06:00"/>
  <performer>
    <function>
      <coding>
        <system
                value="http://terminology.hl7.org/CodeSystem/v3-ParticipationType"/>
        <code value="PRF"/>
        <display value="Performer"/>
      </coding>
    </function>
    <actor>🔗 
      <reference value="Practitioner/practitioner02"/>
    </actor>
  </performer>
  <note>
    <text
          value="For technical reasons, PIK3CB was deemed uncallable using this method."/>
  </note>
</Procedure>