Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT 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

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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="generated"/>
    <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><a name="analysisTumorNormalDNA-en-US"> </a><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>: For technical reasons, BCR gene was deemed uncallable.</p></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://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-change-type">
    <valueCodeableConcept>
      <coding>
        <system value="http://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>