Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

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-cibuild 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-analysis2 - XML Representation

Page standards status: Informative

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    <Procedure xmlns="http://hl7.org/fhir">
      <id value="lungMass-analysis2"/>
      <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 class="res-header-id"><b>Generated Narrative: Procedure lungMass-analysis2</b></p><a name="lungMass-analysis2"> </a><a name="hclungMass-analysis2"> </a><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"/><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>: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs deletion-duplication-analysis}">Deletion/duplication analysis</span></p><p><b>Genomic Study Analysis Source Class</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p><p><b>Genomic Study Analysis Change Type</b>: <span title="Codes:{http://www.sequenceontology.org SO:0001019}">CNV</span></p><p><b>Genomic Study Analysis Genome Build</b>: <span title="Codes:{http://loinc.org LA26806-2}">GRCh38</span></p><p><b>Genomic Study Analysis 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>Genomic Study Analysis 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><blockquote><p><b>Genomic Study Analysis Regions</b></p><ul><li>studied: <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></li><li>called: <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></li></ul></blockquote><blockquote><p><b>Genomic Study Analysis Output</b></p><ul><li>type: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs vcf}">VCF</span></li><li>file: <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></li></ul></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>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</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>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><span title="Codes:{http://terminology.hl7.org/CodeSystem/v3-ParticipationType PRF}">Performer</span></td><td><a href="Practitioner-practitioner02.html">Practitioner Jane Doel </a></td></tr></table><p><b>note</b>: </p><blockquote><div><p>For technical reasons, PIK3CB was deemed uncallable using this method.</p>
    </div></blockquote></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="deletion-duplication-analysis"/>
            <display value="Deletion/duplication analysis"/>
          </coding>
        </valueCodeableConcept>
      </extension>
      <extension
                 url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genomic-source-class">
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA6684-0"/>
            <display value="Somatic"/>
          </coding>
        </valueCodeableConcept>
      </extension>
      <extension
                 url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type">
        <valueCodeableConcept>
          <coding>
            <system value="http://www.sequenceontology.org"/>
            <code value="SO:0001019"/>
            <display value="CNV"/>
          </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-regions">
        <extension url="studied">
          <valueReference>🔗
            <reference value="DocumentReference/WES-FullSequencedRegion-GRCh38"/>
          </valueReference>
        </extension>
        <extension url="called">
          <valueReference>🔗
            <reference value="DocumentReference/CNVAnalysis-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-cnv"/>
          </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>