Genomics Reporting Implementation Guide
3.0.0 - release 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 3.0.0 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

: PGxGenomicReportEMERGE - XML Representation

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<DiagnosticReport xmlns="http://hl7.org/fhir">
  <id value="PGxGenomicReportEMERGE"/>
  <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 PGxGenomicReportEMERGE</b></p><a name="PGxGenomicReportEMERGE"> </a><a name="hcPGxGenomicReportEMERGE"> </a><a name="PGxGenomicReportEMERGE-en-US"> </a><h2><span title="Codes:{http://loinc.org 51969-4}, {http://example.org/hgsc.bcm.edu/lab-test-codes/ emerge-seq-ngs-pnl}">Genetic analysis report</span> (<span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span>) </h2><table class="grid"><tr><td>Subject</td><td>Adam B. Everyman  Male, DoB: 1951-01-20 ( Medical Record Number: m123 (use: usual, ))</td></tr><tr><td>When For</td><td>2020-01-01 00:00:00-0500</td></tr><tr><td>Reported</td><td>2020-01-01 00:00:00-0500</td></tr><tr><td>Performer</td><td> <a href="Organization-ExampleOrg.html">Organization some lab</a></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></tr><tr><td><a href="Observation-TxImp01.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>2019-04-01</td></tr><tr><td><a href="Observation-TxImp02.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>2019-04-01</td></tr><tr><td><a href="Observation-TxImp03.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>2019-04-01</td></tr><tr><td><a href="Observation-TxImp04.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>2019-04-01</td></tr><tr><td><a href="Observation-TxImp05.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>2019-04-01</td></tr><tr><td><a href="Observation-TxImp06.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>2019-04-01</td></tr><tr><td><a href="Observation-Pgx-geno-1001.html"><span title="Codes:{http://loinc.org 84413-4}">Genotype display name</span></a></td><td><span title="Codes:{http://www.ncbi.nlm.nih.gov/clinvar 638797}">CYP2C19*2/*2</span></td><td>Final</td><td/><td>2019-04-01</td></tr><tr><td><a href="Observation-Pgx-geno-1003.html"><span title="Codes:{http://loinc.org 84413-4}">Genotype display name</span></a></td><td><span title="Codes:">VKORC1 rs9923231 C/T</span></td><td>Final</td><td/><td>2019-04-01</td></tr><tr><td><a href="Observation-Pgx-geno-1002.html"><span title="Codes:{http://loinc.org 84413-4}">Genotype display name</span></a></td><td><span title="Codes:">CYP2C9*1/*1</span></td><td>Final</td><td/><td>2019-04-01</td></tr><tr><td><a href="Observation-Pgx-var-1011.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>2020-01-01</td></tr><tr><td><a href="Observation-Pgx-var-1012.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>2019-04-01</td></tr><tr><td><a href="Observation-Pgx-var-1013.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>2019-04-01</td></tr><tr><td><a href="Observation-Pgx-var-1014.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>2019-04-01</td></tr><tr><td><a href="Observation-Pgx-var-1015.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>2019-04-01</td></tr><tr><td><a href="Observation-Pgx-var-1016.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>2019-04-01</td></tr><tr><td><a href="Observation-Pgx-var-1017.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>2019-04-01</td></tr><tr><td><a href="Observation-Pgx-var-1018.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>2019-04-01</td></tr><tr><td><a href="Observation-Pgx-var-1019.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>This variant was confirmed with SANGER sequencing</td><td>2019-04-01</td></tr><tr><td><a href="Observation-Pgx-var-1020.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>This variant was confirmed with SANGER sequencing</td><td>2019-04-01</td></tr><tr><td><a href="Observation-Pgx-var-1021.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>This variant was confirmed with SANGER sequencing</td><td>2019-04-01</td></tr></table><p>Based on the genotype result, this patient is predicted to have a CYP2C19 poor metabolizer phenotype. This genotype information can be used by patients and clinicians as part of the shared decision-making process for several drugs metabolized by CYP2C19 including clopidogrel, voriconazole, amitriptyline, citalopram and escitalopram.</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/PGXGenomicStudy"/>
    </valueReference>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action">
    <valueReference>🔗 
      <reference value="Task/PGxRecEx01"/>
      <display value="No clopidogrel"/>
    </valueReference>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action">
    <valueReference>🔗 
      <reference value="Task/PGxRecEx02"/>
      <display value="No voriconazole"/>
    </valueReference>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action">
    <valueReference>🔗 
      <reference value="Task/PGxRecEx03"/>
      <display value="50% citalopram"/>
    </valueReference>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action">
    <valueReference>🔗 
      <reference value="Task/PGxRecEx04"/>
      <display value="50% escitalopram"/>
    </valueReference>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action">
    <valueReference>🔗 
      <reference value="Task/PGxRecEx04"/>
      <display value="50% amitriptyline"/>
    </valueReference>
  </extension>
  <extension
             url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note">
    <valueAnnotation>
      <extension
                 url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code">
        <valueCodeableConcept>
          <coding>
            <system
                    value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/coded-annotation-types-cs"/>
            <code value="test-disclaimer"/>
          </coding>
        </valueCodeableConcept>
      </extension>
      <text
            value="This test was developed and its performance determined by this laboratory. It has not been cleared or approved by U.S. Food and Drug Administration.
Since FDA Approval is not required for clinical use of this test, this laboratory has established and validated the test's accuracy and precision,
pursuant to the requirement of CLIA '88. This laboratory is licensed and/or accredited under CLIA and CAP (CAP# xxxxxxx / CLIA# xxxxxxxxxx)."/>
    </valueAnnotation>
  </extension>
  <basedOn>🔗 
    <reference value="ServiceRequest/eMERGEServiceRequest"/>
  </basedOn>
  <status value="final"/>
  <category>
    <coding>
      <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
      <code value="GE"/>
    </coding>
  </category>
  <code>
    <coding>
      <system value="http://loinc.org"/>
      <code value="51969-4"/>
    </coding>
    <coding>
      <system value="http://example.org/hgsc.bcm.edu/lab-test-codes/"/>
      <code value="emerge-seq-ngs-pnl"/>
    </coding>
  </code>
  <subject>🔗 
    <reference value="Patient/CGPatientExample01"/>
  </subject>
  <effectiveDateTime value="2020-01-01T00:00:00-05:00"/>
  <issued value="2020-01-01T00:00:00-05:00"/>
  <performer>🔗 
    <reference value="Organization/ExampleOrg"/>
  </performer>
  <result>🔗 
    <reference value="Observation/TxImp01"/>
    <display value="clopidogrel, poor metabolizer"/>
  </result>
  <result>🔗 
    <reference value="Observation/TxImp02"/>
    <display value="voriconazole, poor metabolizer"/>
  </result>
  <result>🔗 
    <reference value="Observation/TxImp03"/>
    <display value="citalopram, poor metabolizer"/>
  </result>
  <result>🔗 
    <reference value="Observation/TxImp04"/>
    <display value="escitalopram, poor metabolizer"/>
  </result>
  <result>🔗 
    <reference value="Observation/TxImp05"/>
    <display value="amitriptyline, poor metabolizer"/>
  </result>
  <result>🔗 
    <reference value="Observation/TxImp06"/>
    <display value="medium sensitivity to warfarin"/>
  </result>
  <result>🔗 
    <reference value="Observation/Pgx-geno-1001"/>
    <display value="CYP2C19*2/*2"/>
  </result>
  <result>🔗 
    <reference value="Observation/Pgx-geno-1003"/>
    <display value="VKORC1 rs9923231 C/T"/>
  </result>
  <result>🔗 
    <reference value="Observation/Pgx-geno-1002"/>
    <display value="CYP2C9*1/*1"/>
  </result>
  <result>🔗 
    <reference value="Observation/Pgx-var-1011"/>
    <display value="NC_000010.10(CYP2C19):g.96521657C="/>
  </result>
  <result>🔗 
    <reference value="Observation/Pgx-var-1012"/>
    <display value="NC_000010.10(CYP2C19):g.96522463A="/>
  </result>
  <result>🔗 
    <reference value="Observation/Pgx-var-1013"/>
    <display value="NC_000010.10(CYP2C19):g.96535173T="/>
  </result>
  <result>🔗 
    <reference value="Observation/Pgx-var-1014"/>
    <display value="NC_000010.10(CYP2C19):g.96535210G="/>
  </result>
  <result>🔗 
    <reference value="Observation/Pgx-var-1015"/>
    <display value="NC_000010.10(CYP2C19):g.96540410G&gt;A"/>
  </result>
  <result>🔗 
    <reference value="Observation/Pgx-var-1016"/>
    <display value="NC_000010.10(CYP2C19):g.96541616G="/>
  </result>
  <result>🔗 
    <reference value="Observation/Pgx-var-1017"/>
    <display value="NC_000010.10(CYP2C19):g.96541756T="/>
  </result>
  <result>🔗 
    <reference value="Observation/Pgx-var-1018"/>
    <display value="NC_000010.10(CYP2C19):g.96612495C="/>
  </result>
  <result>🔗 
    <reference value="Observation/Pgx-var-1019"/>
    <display value="NC_000016.9(VKORC1):g.31096368C&gt;T"/>
  </result>
  <result>🔗 
    <reference value="Observation/Pgx-var-1020"/>
    <display value="NC_000010.10(CYP2C9):g.96702047C="/>
  </result>
  <result>🔗 
    <reference value="Observation/Pgx-var-1021"/>
    <display value="NC_000010.10(CYP2C9):g.96741053A="/>
  </result>
  <conclusion
              value="Based on the genotype result, this patient is predicted to have a CYP2C19 poor metabolizer phenotype. This genotype information can be used by patients and clinicians as part of the shared decision-making process for several drugs metabolized by CYP2C19 including clopidogrel, voriconazole, amitriptyline, citalopram and escitalopram."/>
  <conclusionCode>
    <coding>
      <system value="http://loinc.org"/>
      <code value="LA6576-8"/>
      <display value="Positive"/>
    </coding>
  </conclusionCode>
</DiagnosticReport>