Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions

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: Genomic Study PGx Example

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<GenomicStudy xmlns="http://hl7.org/fhir">
  <id value="example-pgx"/>
  <language value="en"/>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><p class="res-header-id"><b>Generated Narrative: GenomicStudy example-pgx</b></p><a name="example-pgx"> </a><a name="hcexample-pgx"> </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">Language: en</p></div><p><b>identifier</b>: <code>http://example.org/identifiers/genomicstudies</code>/urn:uuid:pgx-study-0001 (use: temp, )</p><p><b>status</b>: Available</p><p><b>type</b>: <span title="Codes:{http://snomed.info/sct 405825005}">Molecular genetic test (procedure)</span></p><p><b>subject</b>: <a href="Patient-pgxPatient.html">Adam B. Everyman (official) Male, DoB: 1951-01-20 ( Medical record number: m123 (use: usual, period: 2021-01-01 --&gt; (ongoing)))</a></p><p><b>startDate</b>: 2021-01-01</p><p><b>basedOn</b>: <a href="ServiceRequest-pgxServiceRequest.html">ServiceRequest </a></p><p><b>interpreter</b>: <a href="Practitioner-practitioner02.html">Practitioner Jane Doel </a></p><h3>Reasons</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Concept</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://snomed.info/sct 182992009}">Treatment completed (situation)</span></td></tr></table><p><b>note</b>: </p><blockquote><div><p>PGX panel ordered prior to initiating warfarin therapy to guide dosing based on CYP2C9 and VKORC1 genotype.</p>
</div></blockquote><p><b>description</b>: </p><div><p>Pharmacogenomics sequencing panel targeting protein-coding and exon-splicing regions of CYP2C19, CYP2C9, and VKORC1 to inform drug selection and dosing.</p>
</div><blockquote><p><b>analysis</b></p><p><b>identifier</b>: <code>http://example.org/identifiers/genomicAnalyses</code>/urn:uuid:pgx-analysis-0001 (use: temp, )</p><p><b>methodType</b>: <span title="Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype sequence-analysis-of-the-entire-coding-region}">Sequence analysis of the entire coding region</span></p><p><b>changeType</b>: <span title="Codes:{http://www.sequenceontology.org SO:0001483}">SNV</span>, <span title="Codes:{http://www.sequenceontology.org SO:0001019}">copy_number_variation</span></p><p><b>genomeBuild</b>: <span title="Codes:{http://loinc.org LA26806-2}">GRCh38</span></p><p><b>genomicSourceClass</b>: <span title="Codes:{http://loinc.org LA6683-2}">Germline</span></p><p><b>title</b>: PGX Targeted Gene Panel - Sequencing Analysis</p><p><b>specimen</b>: <a href="Specimen-pgxSpecimen.html">Specimen: identifier = http://example.org/identifiers/specimens#pgx-spec-001; status = available; type = Blood specimen (specimen); receivedTime = 2020-12-20 10:00:00+0000</a></p><p><b>date</b>: 2021-01-01 01:01:10-0600</p><p><b>note</b>: </p><blockquote><div><p>Sequencing coverage of 100% achieved across all targeted regions.</p>
</div></blockquote><h3>Metrics</h3><table class="grid"><tr><td style="display: none">-</td><td><b>SequencingCoverage</b></td><td><b>Description</b></td></tr><tr><td style="display: none">*</td><td>100 %<span style="background: LightGoldenRodYellow"> (Details: UCUM  code% = '%')</span></td><td>100% coverage of protein-coding and exon-splicing regions for all three genes.</td></tr></table><blockquote><p><b>genomicRegion</b></p><p><b>type</b>: <span title="Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype studied}">Studied</span></p><h3>Locus</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Concept</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://www.genenames.org HGNC:2621}">protein-coding and exon-splicing regions of CYP2C19</span></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://www.genenames.org HGNC:2623}">protein-coding and exon-splicing regions of CYP2C9</span></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://www.genenames.org HGNC:23663}">protein-coding and exon-splicing regions of VKORC1</span></td></tr></table></blockquote><blockquote><p><b>genomicRegion</b></p><p><b>type</b>: <span title="Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype called}">Called</span></p><h3>Locus</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Concept</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://www.genenames.org HGNC:2621}">CYP2C19</span></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://www.genenames.org HGNC:2623}">CYP2C9</span></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://www.genenames.org HGNC:23663}">VKORC1</span></td></tr></table></blockquote><h3>Outputs</h3><table class="grid"><tr><td style="display: none">-</td><td><b>File</b></td><td><b>Type</b></td></tr><tr><td style="display: none">*</td><td><a href="DocumentReference-pgxVCFfile.html">DocumentReference: identifier = http://example.org/identifiers/files#pgx-vcf-001; status = current; docStatus = final; description = VCF file containing PGX variant calls for CYP2C19, CYP2C9, and VKORC1; securityLabel = Restricted</a></td><td><span title="Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat vcf}">VCF</span></td></tr></table><h3>Performers</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Actor</b></td><td><b>Role</b></td></tr><tr><td style="display: none">*</td><td><a href="Practitioner-practitioner02.html">Practitioner Jane Doel </a></td><td><span title="Codes:{http://terminology.hl7.org/CodeSystem/v3-ParticipationType PRF}">Performer</span></td></tr></table><h3>Devices</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Device</b></td><td><b>Function</b></td></tr><tr><td style="display: none">*</td><td><a href="Device-NGS-device.html">Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object)</a></td><td><span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></td></tr></table></blockquote></div>
  </text>
  <!-- 
        Pharmacogenomics (PGX) targeted gene panel study.
        Germline sequencing of CYP2C19, CYP2C9, and VKORC1 protein-coding and
        exon-splicing regions to guide drug dosing decisions.
        Demonstrates: coded gene genomicRegion.studied (HGNC), genomicRegion.called, metrics (sequencing coverage),
        germline genomicSourceClass.
     -->
  <identifier>
    <use value="temp"/>
    <system value="http://example.org/identifiers/genomicstudies"/>
    <value value="urn:uuid:pgx-study-0001"/>
  </identifier>
  <status value="available"/>
  <type>
    <coding>
      <system value="http://snomed.info/sct"/>
      <code value="405825005"/>
      <display value="Molecular genetic test (procedure)"/>
    </coding>
  </type>
  <subject>🔗 
    <reference value="Patient/pgxPatient"/>
  </subject>
  <startDate value="2021-01-01"/>
  <basedOn>🔗 
    <reference value="ServiceRequest/pgxServiceRequest"/>
  </basedOn>
  <interpreter>🔗 
    <reference value="Practitioner/practitioner02"/>
  </interpreter>
  <reason>
    <concept>
      <coding>
        <system value="http://snomed.info/sct"/>
        <code value="182992009"/>
        <display value="Treatment completed (situation)"/>
      </coding>
    </concept>
  </reason>
  <note>
    <text
          value="PGX panel ordered prior to initiating warfarin therapy to guide dosing based on CYP2C9 and VKORC1 genotype."/>
  </note>
  <description
               value="Pharmacogenomics sequencing panel targeting protein-coding and exon-splicing regions of CYP2C19, CYP2C9, and VKORC1 to inform drug selection and dosing."/>
  <analysis>
    <identifier>
      <use value="temp"/>
      <system value="http://example.org/identifiers/genomicAnalyses"/>
      <value value="urn:uuid:pgx-analysis-0001"/>
    </identifier>
    <methodType>
      <coding>
        <system
                value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype"/>
        <code value="sequence-analysis-of-the-entire-coding-region"/>
        <display value="Sequence analysis of the entire coding region"/>
      </coding>
    </methodType>
    <changeType>
      <coding>
        <system value="http://www.sequenceontology.org"/>
        <code value="SO:0001483"/>
        <display value="SNV"/>
      </coding>
    </changeType>
    <changeType>
      <coding>
        <system value="http://www.sequenceontology.org"/>
        <code value="SO:0001019"/>
        <display value="copy_number_variation"/>
      </coding>
    </changeType>
    <genomeBuild>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA26806-2"/>
        <display value="GRCh38"/>
      </coding>
    </genomeBuild>
    <genomicSourceClass>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA6683-2"/>
        <display value="Germline"/>
      </coding>
    </genomicSourceClass>
    <title value="PGX Targeted Gene Panel - Sequencing Analysis"/>
    <specimen>🔗 
      <reference value="Specimen/pgxSpecimen"/>
    </specimen>
    <date value="2021-01-01T01:01:10-06:00"/>
    <note>
      <text
            value="Sequencing coverage of 100% achieved across all targeted regions."/>
    </note>
    <metrics>
      <sequencingCoverage>
        <value value="100"/>
        <unit value="%"/>
        <system value="http://unitsofmeasure.org"/>
        <code value="%"/>
      </sequencingCoverage>
      <description
                   value="100% coverage of protein-coding and exon-splicing regions for all three genes."/>
    </metrics>
    <!--  genomicRegion: studied = all three PGx gene targets (protein-coding and exon-splicing regions)  -->
    <genomicRegion>
      <type>
        <coding>
          <system
                  value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype"/>
          <code value="studied"/>
          <display value="Studied"/>
        </coding>
      </type>
      <locus>
        <concept>
          <coding>
            <system value="http://www.genenames.org"/>
            <code value="HGNC:2621"/>
            <display value="CYP2C19"/>
          </coding>
          <text value="protein-coding and exon-splicing regions of CYP2C19"/>
        </concept>
      </locus>
      <locus>
        <concept>
          <coding>
            <system value="http://www.genenames.org"/>
            <code value="HGNC:2623"/>
            <display value="CYP2C9"/>
          </coding>
          <text value="protein-coding and exon-splicing regions of CYP2C9"/>
        </concept>
      </locus>
      <locus>
        <concept>
          <coding>
            <system value="http://www.genenames.org"/>
            <code value="HGNC:23663"/>
            <display value="VKORC1"/>
          </coding>
          <text value="protein-coding and exon-splicing regions of VKORC1"/>
        </concept>
      </locus>
    </genomicRegion>
    <!--  genomicRegion: called = same three genes, all achieved sufficient coverage to produce calls  -->
    <genomicRegion>
      <type>
        <coding>
          <system
                  value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype"/>
          <code value="called"/>
          <display value="Called"/>
        </coding>
      </type>
      <locus>
        <concept>
          <coding>
            <system value="http://www.genenames.org"/>
            <code value="HGNC:2621"/>
            <display value="CYP2C19"/>
          </coding>
        </concept>
      </locus>
      <locus>
        <concept>
          <coding>
            <system value="http://www.genenames.org"/>
            <code value="HGNC:2623"/>
            <display value="CYP2C9"/>
          </coding>
        </concept>
      </locus>
      <locus>
        <concept>
          <coding>
            <system value="http://www.genenames.org"/>
            <code value="HGNC:23663"/>
            <display value="VKORC1"/>
          </coding>
        </concept>
      </locus>
    </genomicRegion>
    <output>
      <file>🔗 
        <reference value="DocumentReference/pgxVCFfile"/>
      </file>
      <type>
        <coding>
          <system
                  value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"/>
          <code value="vcf"/>
          <display value="VCF"/>
        </coding>
      </type>
    </output>
    <performer>
      <actor>🔗 
        <reference value="Practitioner/practitioner02"/>
      </actor>
      <role>
        <coding>
          <system
                  value="http://terminology.hl7.org/CodeSystem/v3-ParticipationType"/>
          <code value="PRF"/>
          <display value="Performer"/>
        </coding>
      </role>
    </performer>
    <device>
      <device>🔗 
        <reference value="Device/NGS-device"/>
      </device>
      <function>
        <coding>
          <system value="http://loinc.org"/>
          <code value="LA26398-0"/>
          <display value="Sequencing"/>
        </coding>
      </function>
    </device>
  </analysis>
</GenomicStudy>