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

## : somaticReport - XML Representation

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    <DiagnosticReport xmlns="http://hl7.org/fhir">
      <id value="somaticReport"/>
      <meta>
        <profile
                 value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report"/>
      </meta>
      <text>
        <status value="generated"/>
        <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: DiagnosticReport somaticReport</b></p><a name="somaticReport"> </a><a name="hcsomaticReport"> </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-report.html">Genomic Report</a></p></div><h2><span title="Codes:{http://loinc.org 51969-4}">Genetic analysis report</span> (<span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span>) </h2><table class="grid"><tr><td>When For</td><td>2023-02-02</td></tr><tr><td>Performers</td><td> <a href="Practitioner-pathologistPractitioner.html">Practitioner Test Dolin </a> <a href="Organization-performingOrganization.html">Organization My Test Pathology Laboratories</a></td></tr><tr><td>Identifier</td><td> Accession ID/23-0000345</td></tr></table><p><b>Report Details</b></p><table class="grid"><tr><td><b>Code</b></td><td><b>Value</b></td><td><b>Flags</b></td><td><b>Note</b></td><td><b>When For</b></td><td><b>Reported</b></td></tr><tr><td><a href="Observation-NOTCH1-uncertain-var.html"><span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></a></td><td><span title="Codes:{http://loinc.org LA9633-4}">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-ZFHX3-uncertain-var.html"><span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></a></td><td><span title="Codes:{http://loinc.org LA9633-4}">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-MSH2-del-var.html"><span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></a></td><td><span title="Codes:{http://loinc.org LA9633-4}">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-NTHL1-snv-var.html"><span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></a></td><td><span title="Codes:{http://loinc.org LA9633-4}">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-STAG2-insertion-var.html"><span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></a></td><td><span title="Codes:{http://loinc.org LA9633-4}">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-ATR-insertion-var.html"><span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></a></td><td><span title="Codes:{http://loinc.org LA9633-4}">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-EGFR-L858R-var.html"><span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></a></td><td><span title="Codes:{http://loinc.org LA9633-4}">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-ROS1-Fusion-var.html"><span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></a></td><td><span title="Codes:{http://loinc.org LA9633-4}">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-NOTCH1-significance.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-ZFHX3-significance.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-MSH2-del-disease.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-NTHL1-snv-disease.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-STAG2-insertion-significance.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-ATR-insertion-significance.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-EGFR-L858R-significance.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-ROS1-Fusion-disease.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-ROS1-Fusion-therapuTrial.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}">Therapeutic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-ROS1-Fusion-therapuDrug.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}">Therapeutic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-EGFR-L858R-therapuDrug1.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}">Therapeutic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-EGFR-L858R-therapuDrug2.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}">Therapeutic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-TMB-therapuDrug.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}">Therapeutic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-NOTCH1-uncertain-molc.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-ZFHX3-uncertain-molc.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-MSH2-del-molc.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-NTHL1-snv-molc.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-STAG2-insertion-molc.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-ATR-insertion-molc.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-EGFR-L858R-molc.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-ROS1-Fusion.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-TMBExample.html"><span title="Codes:{http://loinc.org 94076-7}">Mutations/Megabase [# Ratio] in Tumor</span></a></td><td>29.8</td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-MSIExample.html"><span title="Codes:{http://loinc.org 81695-9}">Microsatellite instability [Interpretation] in Cancer specimen Qualitative</span></a></td><td><span title="Codes:{http://loinc.org LA26203-2}">MSI-H</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-PDL1Example.html"><span title="Codes:{http://loinc.org 85147-7}">PD-L1 by clone 22C3 in Tissue by Immune stain Report</span></a></td><td><span title="Codes:{http://loinc.org LA6576-8}">Positive</span></td><td>Final</td><td><blockquote><div><p>5% tumor proportion score</p>
    </div></blockquote></td><td>2023-02-01</td><td/></tr><tr><td><a href="Observation-HLA-A-haplotype1.html"><span title="Codes:{http://loinc.org 84414-2}">Haplotype Name</span></a></td><td><span title="Codes:{http://www.ebi.ac.uk/ipd/imgt/hla A*24:02}">HLA-A*24:02</span></td><td>Final</td><td/><td>2023-02-01</td><td>2023-02-01 00:00:00-0500</td></tr><tr><td><a href="Observation-HLA-A-haplotype2.html"><span title="Codes:{http://loinc.org 84414-2}">Haplotype Name</span></a></td><td><span title="Codes:{http://www.ebi.ac.uk/ipd/imgt/hla A*02:06}">HLA-A*02:06</span></td><td>Final</td><td/><td>2023-02-01</td><td>2023-02-01 00:00:00-0500</td></tr><tr><td><a href="Observation-HLA-B-haplotype1.html"><span title="Codes:{http://loinc.org 84414-2}">Haplotype Name</span></a></td><td><span title="Codes:{http://www.ebi.ac.uk/ipd/imgt/hla B*35:01}">HLA-B*35:01</span></td><td>Final</td><td/><td>2023-02-01</td><td>2023-02-01 00:00:00-0500</td></tr><tr><td><a href="Observation-HLA-B-haplotype2.html"><span title="Codes:{http://loinc.org 84414-2}">Haplotype Name</span></a></td><td><span title="Codes:{http://www.ebi.ac.uk/ipd/imgt/hla B*35:01}">HLA-B*35:01</span></td><td>Final</td><td/><td>2023-02-01</td><td>2023-02-01 00:00:00-0500</td></tr><tr><td><a href="Observation-HLA-C-haplotype1.html"><span title="Codes:{http://loinc.org 84414-2}">Haplotype Name</span></a></td><td><span title="Codes:{http://www.ebi.ac.uk/ipd/imgt/hla C*03:03}">HLA-C*03:03</span></td><td>Final</td><td/><td>2023-02-01</td><td>2023-02-01 00:00:00-0500</td></tr><tr><td><a href="Observation-HLA-C-haplotype2.html"><span title="Codes:{http://loinc.org 84414-2}">Haplotype Name</span></a></td><td><span title="Codes:{http://www.ebi.ac.uk/ipd/imgt/hla C*15:02}">HLA-C*15:02</span></td><td>Final</td><td/><td>2023-02-01</td><td>2023-02-01 00:00:00-0500</td></tr></table><p>Patient is positive for Tier 1 / Level A variants, including variants with FDA-approved indications.</p><p><b>Coded Conclusions:</b></p><ul><li><span title="Codes:{http://loinc.org LA6576-8}">Positive</span></li></ul></div>
      </text>
      <extension
                 url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-reference">
        <valueReference>🔗
          <reference value="Procedure/somaticStudy"/>
          <display value="somaticStudy"/>
        </valueReference>
      </extension>
      <identifier>
        <type>
          <coding>
            <system value="http://terminology.hl7.org/CodeSystem/v2-0203"/>
            <code value="ACSN"/>
            <display value="Accession ID"/>
          </coding>
        </type>
        <value value="23-0000345"/>
      </identifier>
      <basedOn>🔗
        <reference value="ServiceRequest/somaticServiceRequest"/>
      </basedOn>
      <status value="final"/>
      <category>
        <coding>
          <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
          <code value="GE"/>
          <display value="Genetics"/>
        </coding>
      </category>
      <code>
        <coding>
          <system value="http://loinc.org"/>
          <code value="51969-4"/>
          <display value="Genetic analysis report"/>
        </coding>
      </code>
      <effectiveDateTime value="2023-02-02"/>
      <performer>🔗
        <reference value="Practitioner/pathologistPractitioner"/>
      </performer>
      <performer>🔗
        <reference value="Organization/performingOrganization"/>
      </performer>
      <resultsInterpreter>🔗
        <reference value="Practitioner/supervisorPractitioner"/>
      </resultsInterpreter>
      <resultsInterpreter>🔗
        <reference value="Organization/performingOrganization"/>
      </resultsInterpreter>
      <result>🔗
        <reference value="Observation/NOTCH1-uncertain-var"/>
      </result>
      <result>🔗
        <reference value="Observation/ZFHX3-uncertain-var"/>
      </result>
      <result>🔗
        <reference value="Observation/MSH2-del-var"/>
      </result>
      <result>🔗
        <reference value="Observation/NTHL1-snv-var"/>
      </result>
      <result>🔗
        <reference value="Observation/STAG2-insertion-var"/>
      </result>
      <result>🔗
        <reference value="Observation/ATR-insertion-var"/>
      </result>
      <result>🔗
        <reference value="Observation/EGFR-L858R-var"/>
      </result>
      <result>🔗
        <reference value="Observation/ROS1-Fusion-var"/>
      </result>
      <result>🔗
        <reference value="Observation/NOTCH1-significance"/>
      </result>
      <result>🔗
        <reference value="Observation/ZFHX3-significance"/>
      </result>
      <result>🔗
        <reference value="Observation/MSH2-del-disease"/>
      </result>
      <result>🔗
        <reference value="Observation/NTHL1-snv-disease"/>
      </result>
      <result>🔗
        <reference value="Observation/STAG2-insertion-significance"/>
      </result>
      <result>🔗
        <reference value="Observation/ATR-insertion-significance"/>
      </result>
      <result>🔗
        <reference value="Observation/EGFR-L858R-significance"/>
      </result>
      <result>🔗
        <reference value="Observation/ROS1-Fusion-disease"/>
      </result>
      <result>🔗
        <reference value="Observation/ROS1-Fusion-therapuTrial"/>
      </result>
      <result>🔗
        <reference value="Observation/ROS1-Fusion-therapuDrug"/>
      </result>
      <result>🔗
        <reference value="Observation/EGFR-L858R-therapuDrug1"/>
      </result>
      <result>🔗
        <reference value="Observation/EGFR-L858R-therapuDrug2"/>
      </result>
      <result>🔗
        <reference value="Observation/TMB-therapuDrug"/>
      </result>
      <result>🔗
        <reference value="Observation/NOTCH1-uncertain-molc"/>
      </result>
      <result>🔗
        <reference value="Observation/ZFHX3-uncertain-molc"/>
      </result>
      <result>🔗
        <reference value="Observation/MSH2-del-molc"/>
      </result>
      <result>🔗
        <reference value="Observation/NTHL1-snv-molc"/>
      </result>
      <result>🔗
        <reference value="Observation/STAG2-insertion-molc"/>
      </result>
      <result>🔗
        <reference value="Observation/ATR-insertion-molc"/>
      </result>
      <result>🔗
        <reference value="Observation/EGFR-L858R-molc"/>
      </result>
      <result>🔗
        <reference value="Observation/ROS1-Fusion"/>
      </result>
      <result>🔗
        <reference value="Observation/TMBExample"/>
      </result>
      <result>🔗
        <reference value="Observation/MSIExample"/>
      </result>
      <result>🔗
        <reference value="Observation/PDL1Example"/>
      </result>
      <result>🔗
        <reference value="Observation/HLA-A-haplotype1"/>
      </result>
      <result>🔗
        <reference value="Observation/HLA-A-haplotype2"/>
      </result>
      <result>🔗
        <reference value="Observation/HLA-B-haplotype1"/>
      </result>
      <result>🔗
        <reference value="Observation/HLA-B-haplotype2"/>
      </result>
      <result>🔗
        <reference value="Observation/HLA-C-haplotype1"/>
      </result>
      <result>🔗
        <reference value="Observation/HLA-C-haplotype2"/>
      </result>
      <conclusion
                  value="Patient is positive for Tier 1 / Level A variants, including variants with FDA-approved indications."/>
      <conclusionCode>
        <coding>
          <system value="http://loinc.org"/>
          <code value="LA6576-8"/>
          <display value="Positive"/>
        </coding>
      </conclusionCode>
    </DiagnosticReport>