Genomics Reporting Implementation Guide
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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-ballot 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

: lungMass - XML Representation

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<GenomicStudy xmlns="http://hl7.org/fhir">
  <id value="lungMass"/>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: GenomicStudy lungMass</b></p><a name="lungMass"> </a><a name="hclungMass"> </a><p><b>status</b>: Available</p><p><b>type</b>: <span title="Codes:">Solid tumor whole exome sequencing panel</span></p><p><b>subject</b>: <a href="Patient-genomicPatient.html">John Junior Doe (official) Unknown, DoB: 2001-01-01 ( Medical record number: 11117 (use: temp, period: 2021-01-01 --&gt; (ongoing)))</a></p><p><b>startDate</b>: 2019-03-01</p><p><b>basedOn</b>: <a href="ServiceRequest-genomicServiceRequest.html">ServiceRequest Molecular genetic test (procedure)</a></p><p><b>interpreter</b>: <a href="Practitioner-practitioner02.html">Practitioner Jane Doel </a></p><h3>Reasons</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Concept</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://snomed.info/sct 309529002}">Lung mass (finding)</span></td></tr></table><p><b>note</b>: </p><blockquote><div><p>For technical reasons, PIK3CB was deemed uncallable.</p>
</div></blockquote><blockquote><p><b>analysis</b></p><p><b>methodType</b>: <span title="Codes:{http://hl7.org/fhir/genomicstudy-methodtype sequence-analysis-of-the-entire-coding-region}">Sequence analysis of the entire coding region</span></p><p><b>changeType</b>: <span title="Codes:{http://www.sequenceontology.org SO:0001483}">SNV</span>, <span title="Codes:{http://www.sequenceontology.org SO:0002007}">MNV</span>, <span title="Codes:{http://www.sequenceontology.org SO:1000032}">delins</span></p><p><b>genomeBuild</b>: <span title="Codes:{http://loinc.org LA26806-2}">GRCh38</span></p><p><b>instantiatesUri</b>: <a href="https://pubmed.ncbi.nlm.nih.gov/33927380/">https://pubmed.ncbi.nlm.nih.gov/33927380/</a></p><p><b>focus</b>: <a href="Patient-genomicPatient.html">John Junior Doe (official) Unknown, DoB: 2001-01-01 ( Medical record number: 11117 (use: temp, period: 2021-01-01 --&gt; (ongoing)))</a></p><p><b>specimen</b>: <a href="Specimen-genomicSpecimen.html">Specimen: identifier = http://example.org/identifiers/specimens#4; status = available; type = Specimen from lung obtained by biopsy (specimen); receivedTime = 2019-03-01 01:01:01+0000</a></p><p><b>date</b>: 2019-03-01 01:01:10-0600</p><p><b>note</b>: </p><blockquote><div><p>For technical reasons, PIK3CB was deemed uncallable using this method.</p>
</div></blockquote><p><b>regionsStudied</b>: <a href="DocumentReference-WES-FullSequencedRegion-GRCh38.html">DocumentReference: identifier = http://example.org/identifiers/files#11117; status = current; docStatus = preliminary; description = WES_FullSequencedRegion_GRCh38: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></p><p><b>regionsCalled</b>: <a href="DocumentReference-SimpleVariantAnalysis-called.html">DocumentReference: identifier = http://example.org/identifiers/files#11118; status = current; docStatus = preliminary; description = SimpleVariantAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></p><h3>Outputs</h3><table class="grid"><tr><td style="display: none">-</td><td><b>File</b></td><td><b>Type</b></td></tr><tr><td style="display: none">*</td><td><a href="DocumentReference-genomicVCFfile-simple.html">DocumentReference: identifier = http://example.org/identifiers/files#11119; status = current; docStatus = preliminary; description = genomicVCFfile_simple: A sample Document Reference instance representing a VCF file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></td><td><span title="Codes:{http://hl7.org/fhir/genomicstudy-dataformat vcf}">VCF</span></td></tr></table><h3>Performers</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Actor</b></td><td><b>Role</b></td></tr><tr><td style="display: none">*</td><td><a href="Practitioner-practitioner02.html">Practitioner Jane Doel </a></td><td><span title="Codes:{http://terminology.hl7.org/CodeSystem/v3-ParticipationType PRF}">Performer</span></td></tr></table><h3>Devices</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Device</b></td></tr><tr><td style="display: none">*</td><td><a href="Device-triodenovo-software.html">Device: identifier = http://example.org/identifiers/devices#11112; status = active; manufacturer = Vanderbilt Genetics Institute; type = Software (physical object)</a></td></tr></table></blockquote><blockquote><p><b>analysis</b></p><p><b>methodType</b>: <span title="Codes:{http://hl7.org/fhir/genomicstudy-methodtype deletion-duplication-analysis}">Deletion/duplication analysis</span></p><p><b>changeType</b>: <span title="Codes:{http://www.sequenceontology.org SO:0001019}">CNV</span></p><p><b>genomeBuild</b>: <span title="Codes:{http://loinc.org LA26806-2}">GRCh38</span></p><p><b>instantiatesUri</b>: <a href="https://pubmed.ncbi.nlm.nih.gov/33927380/">https://pubmed.ncbi.nlm.nih.gov/33927380/</a></p><p><b>focus</b>: <a href="Patient-genomicPatient.html">John Junior Doe (official) Unknown, DoB: 2001-01-01 ( Medical record number: 11117 (use: temp, period: 2021-01-01 --&gt; (ongoing)))</a></p><p><b>specimen</b>: <a href="Specimen-genomicSpecimen.html">Specimen: identifier = http://example.org/identifiers/specimens#4; status = available; type = Specimen from lung obtained by biopsy (specimen); receivedTime = 2019-03-01 01:01:01+0000</a></p><p><b>date</b>: 2019-03-01 01:01:10-0600</p><p><b>note</b>: </p><blockquote><div><p>For technical reasons, PIK3CB was deemed uncallable using this method.</p>
</div></blockquote><p><b>regionsStudied</b>: <a href="DocumentReference-WES-FullSequencedRegion-GRCh38.html">DocumentReference: identifier = http://example.org/identifiers/files#11117; status = current; docStatus = preliminary; description = WES_FullSequencedRegion_GRCh38: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></p><p><b>regionsCalled</b>: <a href="DocumentReference-CNVAnalysis-called.html">DocumentReference: identifier = http://example.org/identifiers/files#11120; status = current; docStatus = preliminary; description = CNVAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></p><h3>Outputs</h3><table class="grid"><tr><td style="display: none">-</td><td><b>File</b></td><td><b>Type</b></td></tr><tr><td style="display: none">*</td><td><a href="DocumentReference-genomicVCFfile-cnv.html">DocumentReference: identifier = http://example.org/identifiers/files#11121; status = current; docStatus = preliminary; description = genomicVCFfile_cnv: A sample Document Reference instance representing a VCF file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></td><td><span title="Codes:{http://hl7.org/fhir/genomicstudy-dataformat vcf}">VCF</span></td></tr></table><h3>Performers</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Actor</b></td><td><b>Role</b></td></tr><tr><td style="display: none">*</td><td><a href="Practitioner-practitioner02.html">Practitioner Jane Doel </a></td><td><span title="Codes:{http://terminology.hl7.org/CodeSystem/v3-ParticipationType PRF}">Performer</span></td></tr></table></blockquote></div>
  </text>
  <status value="available"/>
  <type>
    <text value="Solid tumor whole exome sequencing panel"/>
  </type>
  <subject>🔗 
    <reference value="Patient/genomicPatient"/>
  </subject>
  <startDate value="2019-03-01"/>
  <basedOn>🔗 
    <reference value="ServiceRequest/genomicServiceRequest"/>
  </basedOn>
  <interpreter>🔗 
    <reference value="Practitioner/practitioner02"/>
  </interpreter>
  <reason>
    <concept>
      <coding>
        <system value="http://snomed.info/sct"/>
        <code value="309529002"/>
        <display value="Lung mass (finding)"/>
      </coding>
    </concept>
  </reason>
  <note>
    <text value="For technical reasons, PIK3CB was deemed uncallable."/>
  </note>
  <analysis>
    <methodType>
      <coding>
        <system value="http://hl7.org/fhir/genomicstudy-methodtype"/>
        <code value="sequence-analysis-of-the-entire-coding-region"/>
        <display value="Sequence analysis of the entire coding region"/>
      </coding>
    </methodType>
    <changeType>
      <coding>
        <system value="http://www.sequenceontology.org"/>
        <code value="SO:0001483"/>
        <display value="SNV"/>
      </coding>
    </changeType>
    <changeType>
      <coding>
        <system value="http://www.sequenceontology.org"/>
        <code value="SO:0002007"/>
        <display value="MNV"/>
      </coding>
    </changeType>
    <changeType>
      <coding>
        <system value="http://www.sequenceontology.org"/>
        <code value="SO:1000032"/>
        <display value="delins"/>
      </coding>
    </changeType>
    <genomeBuild>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA26806-2"/>
        <display value="GRCh38"/>
      </coding>
    </genomeBuild>
    <instantiatesUri value="https://pubmed.ncbi.nlm.nih.gov/33927380/"/>
    <focus>🔗 
      <reference value="Patient/genomicPatient"/>
    </focus>
    <specimen>🔗 
      <reference value="Specimen/genomicSpecimen"/>
    </specimen>
    <date value="2019-03-01T01:01:10-06:00"/>
    <note>
      <text
            value="For technical reasons, PIK3CB was deemed uncallable using this method."/>
    </note>
    <regionsStudied>🔗 
      <reference value="DocumentReference/WES-FullSequencedRegion-GRCh38"/>
    </regionsStudied>
    <regionsCalled>🔗 
      <reference value="DocumentReference/SimpleVariantAnalysis-called"/>
    </regionsCalled>
    <output>
      <file>🔗 
        <reference value="DocumentReference/genomicVCFfile-simple"/>
      </file>
      <type>
        <coding>
          <system value="http://hl7.org/fhir/genomicstudy-dataformat"/>
          <code value="vcf"/>
          <display value="VCF"/>
        </coding>
      </type>
    </output>
    <performer>
      <actor>🔗 
        <reference value="Practitioner/practitioner02"/>
      </actor>
      <role>
        <coding>
          <system
                  value="http://terminology.hl7.org/CodeSystem/v3-ParticipationType"/>
          <code value="PRF"/>
          <display value="Performer"/>
        </coding>
      </role>
    </performer>
    <device>
      <device>🔗 
        <reference value="Device/triodenovo-software"/>
      </device>
    </device>
  </analysis>
  <analysis>
    <methodType>
      <coding>
        <system value="http://hl7.org/fhir/genomicstudy-methodtype"/>
        <code value="deletion-duplication-analysis"/>
        <display value="Deletion/duplication analysis"/>
      </coding>
    </methodType>
    <changeType>
      <coding>
        <system value="http://www.sequenceontology.org"/>
        <code value="SO:0001019"/>
        <display value="CNV"/>
      </coding>
    </changeType>
    <genomeBuild>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA26806-2"/>
        <display value="GRCh38"/>
      </coding>
    </genomeBuild>
    <instantiatesUri value="https://pubmed.ncbi.nlm.nih.gov/33927380/"/>
    <focus>🔗 
      <reference value="Patient/genomicPatient"/>
    </focus>
    <specimen>🔗 
      <reference value="Specimen/genomicSpecimen"/>
    </specimen>
    <date value="2019-03-01T01:01:10-06:00"/>
    <note>
      <text
            value="For technical reasons, PIK3CB was deemed uncallable using this method."/>
    </note>
    <regionsStudied>🔗 
      <reference value="DocumentReference/WES-FullSequencedRegion-GRCh38"/>
    </regionsStudied>
    <regionsCalled>🔗 
      <reference value="DocumentReference/CNVAnalysis-called"/>
    </regionsCalled>
    <output>
      <file>🔗 
        <reference value="DocumentReference/genomicVCFfile-cnv"/>
      </file>
      <type>
        <coding>
          <system value="http://hl7.org/fhir/genomicstudy-dataformat"/>
          <code value="vcf"/>
          <display value="VCF"/>
        </coding>
      </type>
    </output>
    <performer>
      <actor>🔗 
        <reference value="Practitioner/practitioner02"/>
      </actor>
      <role>
        <coding>
          <system
                  value="http://terminology.hl7.org/CodeSystem/v3-ParticipationType"/>
          <code value="PRF"/>
          <display value="Performer"/>
        </coding>
      </role>
    </performer>
  </analysis>
</GenomicStudy>