Genomics Reporting Implementation Guide
2.0.0 - trial-use

This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

: PGxGenomicsReportEMERGE - XML Representation

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<DiagnosticReport xmlns="http://hl7.org/fhir">
  <id value="PGxGenomicsReportEMERGE"/>
  <meta>
    <profile
             value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report"/>
  </meta>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><h2><span title="Codes: {https://hgsc.bcm.edu/lab-test-codes/ emerge-seq-ngs-pnl}">emerge-seq-ngs-pnl</span> (<span title="Codes: {http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span>) </h2><table class="grid"><tr><td>Subject</td><td><b>Adam B. Everyman </b> male, DoB: 1951-01-20 ( Medical Record Number: m123 (USUAL))</td></tr><tr><td>When For</td><td>2020-01-01 12:00:00-0500</td></tr><tr><td>Reported</td><td>2020-01-01 12:00:00-0500</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>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><td></td><td></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><td></td><td></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><td></td><td></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><td></td><td></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><td></td><td></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><td></td><td></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></td><td>2020-01-01</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></td><td>2020-01-01</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></td><td>2020-01-01</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></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></td><td>2020-01-01</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></td><td>2020-01-01</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></td><td>2020-01-01</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></td><td>2020-01-01</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></td><td>2020-01-01</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></td><td>2020-01-01</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></td><td>2020-01-01</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>This variant was confirmed with SANGER sequencing</td><td>2020-01-01</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>This variant was confirmed with SANGER sequencing</td><td>2020-01-01</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>This variant was confirmed with SANGER sequencing</td><td>2020-01-01</td></tr><tr><td><a href="Observation-RegionStudiedPGx1.html"><span title="Codes: {http://loinc.org 53041-0}">DNA region of interest panel</span></a></td><td></td><td></td><td></td></tr><tr><td><a href="Observation-RegionStudiedPGx2.html"><span title="Codes: {http://loinc.org 53041-0}">DNA region of interest panel</span></a></td><td></td><td></td><td></td></tr><tr><td><a href="Observation-RegionStudiedPGx3.html"><span title="Codes: {http://loinc.org 53041-0}">DNA region of interest panel</span></a></td><td></td><td></td><td></td></tr><tr><td><a href="Observation-OverallInterpExample2.html"><span title="Codes: {http://loinc.org 51968-6}">Discrete variation analysis overall interpretation</span></a></td><td><span title="Codes: {http://loinc.org LA6576-8}">Positive</span></td><td></td><td></td></tr></table></div>
  </text>
  <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/genomics-file">
    <valueReference>
      <reference value="DocumentReference/VCFFile"/>
    </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="https://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>
  <result>
    <reference value="Observation/RegionStudiedPGx1"/>
    <display value="CYP2C19"/>
  </result>
  <result>
    <reference value="Observation/RegionStudiedPGx2"/>
    <display value="CYP2C9"/>
  </result>
  <result>
    <reference value="Observation/RegionStudiedPGx3"/>
    <display value="VKORC1"/>
  </result>
  <result>
    <reference value="Observation/OverallInterpExample2"/>
    <display value="gene-drug interactions found."/>
  </result>
</DiagnosticReport>