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

: somaticReport - XML Representation

Raw xml | Download



<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><a name="somaticReport-en-US"> </a><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>5% tumor proportion score</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>