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

## : analysisTumorNormalDNA - XML Representation

Page standards status: Informative

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    <Procedure xmlns="http://hl7.org/fhir">
      <id value="analysisTumorNormalDNA"/>
      <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 analysisTumorNormalDNA</b></p><a name="analysisTumorNormalDNA"> </a><a name="hcanalysisTumorNormalDNA"> </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><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>studied: <span title="Codes:{http://www.genenames.org HGNC:76}">ABL1</span></li><li>studied: <span title="Codes:{http://www.genenames.org HGNC:427}">ALK</span></li><li>studied: <span title="Codes:{http://www.genenames.org HGNC:583}">APC</span></li><li>uncalled: <a href="DocumentReference-WES-UncallableRegions-GRCh38.html">DocumentReference: identifier = http://example.org/identifiers/files#11146520; status = current; docStatus = preliminary; description = Regions deemed uncallable (generally due to low coverage).; securityLabel = Restricted</a></li></ul></blockquote><p><b>Genomic Study Analysis Method Type</b>: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs sequence-analysis-of-the-entire-coding-region}">Sequence analysis of the entire coding region</span></p><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 Change Type</b>: <span title="Codes:{http://www.sequenceontology.org SO:0001483}">SNV</span></p><p><b>Genomic Study Analysis Change Type</b>: <span title="Codes:{http://www.sequenceontology.org SO:0002007}">MNV</span></p><p><b>Genomic Study Analysis Change Type</b>: <span title="Codes:{http://www.sequenceontology.org SO:1000032}">delins</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-tumorSpecimen.html">Specimen: identifier = http://example.org/identifiers/specimens#222333; status = available; type = Specimen from lung obtained by biopsy (specimen); receivedTime = 2023-01-23 01:01:01+0000; note = Tumor: 20%</a></p><p><b>Genomic Study Analysis Specimen</b>: <a href="Specimen-normalSpecimen.html">Specimen: identifier = http://example.org/identifiers/specimens#444555; status = available; type = Blood specimen (specimen); receivedTime = 2023-01-23 01:01:01+0000</a></p><p><b>Genomic Study Analysis Focus</b>: <a href="Patient-somaticPatient.html">Substance Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567 (use: temp, period: 2021-01-01 --&gt; (ongoing)))</a></p><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-somaticVCFfile.html">DocumentReference: identifier = http://example.org/identifiers/files#1134121; status = current; docStatus = preliminary; description = VCF file containing identified variants; securityLabel = Restricted</a></li></ul></blockquote><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-somaticPatient.html">Substance Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567 (use: temp, period: 2021-01-01 --&gt; (ongoing)))</a></p><p><b>performed</b>: 2023-02-02 01:01:10-0600</p><p><b>note</b>: </p><blockquote><div><p>For technical reasons, BCR gene was deemed uncallable.</p>
    </div></blockquote></div>
      </text>
      <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="studied">
          <valueCodeableConcept>
            <coding>
              <system value="http://www.genenames.org"/>
              <code value="HGNC:76"/>
              <display value="ABL1"/>
            </coding>
          </valueCodeableConcept>
        </extension>
        <extension url="studied">
          <valueCodeableConcept>
            <coding>
              <system value="http://www.genenames.org"/>
              <code value="HGNC:427"/>
              <display value="ALK"/>
            </coding>
          </valueCodeableConcept>
        </extension>
        <extension url="studied">
          <valueCodeableConcept>
            <coding>
              <system value="http://www.genenames.org"/>
              <code value="HGNC:583"/>
              <display value="APC"/>
            </coding>
          </valueCodeableConcept>
        </extension>
        <extension url="uncalled">
          <valueReference>🔗
            <reference value="DocumentReference/WES-UncallableRegions-GRCh38"/>
          </valueReference>
        </extension>
      </extension>
      <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-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-change-type">
        <valueCodeableConcept>
          <coding>
            <system value="http://www.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://www.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://www.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-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/tumorSpecimen"/>
        </valueReference>
      </extension>
      <extension
                 url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen">
        <valueReference>🔗
          <reference value="Specimen/normalSpecimen"/>
        </valueReference>
      </extension>
      <extension
                 url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus">
        <valueReference>🔗
          <reference value="Patient/somaticPatient"/>
        </valueReference>
      </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/somaticVCFfile"/>
          </valueReference>
        </extension>
      </extension>
      <status value="completed"/>
      <category>
        <coding>
          <system
                  value="http://terminology.hl7.org/CodeSystem/observation-category"/>
          <code value="laboratory"/>
        </coding>
      </category>
      <subject>🔗
        <reference value="Patient/somaticPatient"/>
      </subject>
      <performedDateTime value="2023-02-02T01:01:10-06:00"/>
      <note>
        <text value="For technical reasons, BCR gene was deemed uncallable."/>
      </note>
    </Procedure>