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

: bundle-pgxexample - XML Representation

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<Bundle xmlns="http://hl7.org/fhir">
  <id value="bundle-pgxexample"/>
  <type value="transaction"/>
  <entry>
    <fullUrl value="http://example.org/fhir/DiagnosticReport/pgx-report"/>
    <resource>
      <DiagnosticReport>
        <id value="pgx-report"/>
        <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"><a name="DiagnosticReport_pgx-report"> </a><p class="res-header-id"><b>Generated Narrative: DiagnosticReport pgx-report</b></p><a name="pgx-report"> </a><a name="hcpgx-report"> </a><a name="hcpgx-report-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>Subject</td><td>No display for Patient </td></tr><tr><td>When For</td><td>2016</td></tr><tr><td>Reported</td><td>2018-03-06 00:00:00-0500</td></tr><tr><td>Performer</td><td> <a href="Organization-ExampleLab.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></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr></table></div>
        </text>
        <extension
                   url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action">
          <valueReference>
            <reference value="Task/med-usage-impact-task-pgx-example"/>
          </valueReference>
        </extension>
        <basedOn>
          <reference value="ServiceRequest/pgx-request"/>
        </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>
        </code>
        <subject>🔗 
          <reference value="Patient/ExamplePatient"/>
        </subject>
        <effectiveDateTime value="2016"/>
        <issued value="2018-03-06T00:00:00-05:00"/>
        <performer>🔗 
          <reference value="Organization/ExampleLab"/>
        </performer>
        <result>
          <reference value="Observation/med-impact-pgx-example"/>
          <display
                   value="genetics impact for medication metabolism accessment"/>
        </result>
        <result>
          <reference value="Observation/genotype-pgx-example"/>
        </result>
        <result>
          <reference value="Observation/haplotype-1-pgx-example"/>
        </result>
        <result>
          <reference value="Observation/haplotype-2-pgx-example"/>
        </result>
        <result>
          <reference value="Observation/variant-1-pgx-example"/>
        </result>
        <result>
          <reference value="Observation/variant-2-pgx-example"/>
        </result>
      </DiagnosticReport>
    </resource>
    <request>
      <method value="POST"/>
      <url value="DiagnosticReport"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="http://example.org/fhir/Patient/ExamplePatient"/>
    <resource>
      <Patient>
        <id value="ExamplePatient"/>
        <text>
          <status value="additional"/>
          <div xmlns="http://www.w3.org/1999/xhtml">This would contain patient identifiers, demographics, etc.</div>
        </text>
      </Patient>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Patient"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="http://example.org/fhir/Specimen/ExampleSpecimen"/>
    <resource>
      <Specimen>
        <id value="ExampleSpecimen"/>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Specimen_ExampleSpecimen"> </a><p class="res-header-id"><b>Generated Narrative: Specimen ExampleSpecimen</b></p><a name="ExampleSpecimen"> </a><a name="hcExampleSpecimen"> </a><a name="hcExampleSpecimen-en-US"> </a><p><b>subject</b>: <a href="Patient-ExamplePatient.html">Anonymous Patient (no stated gender), DoB Unknown</a></p></div>
        </text>
        <subject>🔗 
          <reference value="Patient/ExamplePatient"/>
        </subject>
      </Specimen>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Specimen"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="http://example.org/fhir/Organization/ExampleLab"/>
    <resource>
      <Organization>
        <id value="ExampleLab"/>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Organization_ExampleLab"> </a><p class="res-header-id"><b>Generated Narrative: Organization ExampleLab</b></p><a name="ExampleLab"> </a><a name="hcExampleLab"> </a><a name="hcExampleLab-en-US"> </a><p><b>name</b>: Some lab</p></div>
        </text>
        <name value="Some lab"/>
      </Organization>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Organization"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="http://example.org/fhir/ServiceRequest/pgx-request"/>
    <resource>
      <ServiceRequest>
        <id value="pgx-request"/>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="ServiceRequest_pgx-request"> </a><p class="res-header-id"><b>Generated Narrative: ServiceRequest pgx-request</b></p><a name="pgx-request"> </a><a name="hcpgx-request"> </a><a name="hcpgx-request-en-US"> </a><p><b>status</b>: Active</p><p><b>intent</b>: Original Order</p><p><b>code</b>: <span title="Codes:{http://loinc.org 51969-4}">Genetic analysis report</span></p><p><b>subject</b>: <a href="Patient-ExamplePatient.html">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>reasonCode</b>: <span title="Codes:">Worried about family planning</span></p></div>
        </text>
        <status value="active"/>
        <intent value="original-order"/>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="51969-4"/>
          </coding>
        </code>
        <subject>🔗 
          <reference value="Patient/ExamplePatient"/>
        </subject>
        <reasonCode>
          <text value="Worried about family planning"/>
        </reasonCode>
      </ServiceRequest>
    </resource>
    <request>
      <method value="POST"/>
      <url value="ServiceRequest"/>
    </request>
  </entry>
  <entry>
    <fullUrl
             value="http://example.org/fhir/Observation/med-impact-pgx-example"/>
    <resource>
      <Observation>
        <id value="med-impact-pgx-example"/>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_med-impact-pgx-example"> </a><p class="res-header-id"><b>Generated Narrative: Observation med-impact-pgx-example</b></p><a name="med-impact-pgx-example"> </a><a name="hcmed-impact-pgx-example"> </a><a name="hcmed-impact-pgx-example-en-US"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}">Therapeutic Implication</span></p><p><b>subject</b>: <a href="Patient-ExamplePatient.html">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href="Organization-ExampleLab.html">Organization Some lab</a></p><p><b>derivedFrom</b>: <a href="Bundle-bundle-pgxexample.html#Observation_genotype-pgx-example">Bundle: type = transaction</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}">Therapeutic Implication</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA25390-8}">Rapid metabolizer</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51963-7}">Medication assessed</span></p><p><b>value</b>: <span title="Codes:{http://www.nlm.nih.gov/research/umls/rxnorm 103}">mercaptopurine</span></p></blockquote></div>
        </text>
        <status value="final"/>
        <category>
          <coding>
            <system
                    value="http://terminology.hl7.org/CodeSystem/observation-category"/>
            <code value="laboratory"/>
          </coding>
        </category>
        <category>
          <coding>
            <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
            <code value="GE"/>
          </coding>
        </category>
        <code>
          <coding>
            <system
                    value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
            <code value="therapeutic-implication"/>
            <display value="Therapeutic Implication"/>
          </coding>
        </code>
        <subject>🔗 
          <reference value="Patient/ExamplePatient"/>
        </subject>
        <effectiveDateTime value="2018"/>
        <issued value="2018-03-06T00:00:00-05:00"/>
        <performer>🔗 
          <reference value="Organization/ExampleLab"/>
        </performer>
        <derivedFrom>
          <reference value="Observation/genotype-pgx-example"/>
        </derivedFrom>
        <component>
          <code>
            <coding>
              <system
                      value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
              <code value="therapeutic-implication"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://loinc.org"/>
              <code value="LA25390-8"/>
              <display value="Rapid metabolizer"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="51963-7"/>
              <display value="Medication assessed"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.nlm.nih.gov/research/umls/rxnorm"/>
              <code value="103"/>
              <display value="mercaptopurine"/>
            </coding>
          </valueCodeableConcept>
        </component>
      </Observation>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl
             value="http://example.org/fhir/Observation/genotype-pgx-example"/>
    <resource>
      <Observation>
        <id value="genotype-pgx-example"/>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_genotype-pgx-example"> </a><p class="res-header-id"><b>Generated Narrative: Observation genotype-pgx-example</b></p><a name="genotype-pgx-example"> </a><a name="hcgenotype-pgx-example"> </a><a name="hcgenotype-pgx-example-en-US"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://loinc.org 84413-4}">genotype display name</span></p><p><b>subject</b>: <a href="Patient-ExamplePatient.html">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href="Organization-ExampleLab.html">Organization Some lab</a></p><p><b>value</b>: <span title="Codes:{http://www.pharmvar.org &quot;CYP2C9}">CYP2C9 *4/*35B</span></p><p><b>specimen</b>: <a href="Specimen-ExampleSpecimen.html">Specimen</a></p><p><b>derivedFrom</b>: </p><ul><li><a href="Bundle-bundle-pgxexample.html#Observation_haplotype-1-pgx-example">Bundle: type = transaction</a></li><li><a href="Bundle-bundle-pgxexample.html#Observation_haplotype-2-pgx-example">Bundle: type = transaction</a></li></ul><h3>Components</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://loinc.org 48018-6}">Gene studied ID</span></td><td><span title="Codes:{http://www.genenames.org HGNC:2623}">CYP2C9</span></td></tr></table></div>
        </text>
        <status value="final"/>
        <category>
          <coding>
            <system
                    value="http://terminology.hl7.org/CodeSystem/observation-category"/>
            <code value="laboratory"/>
          </coding>
        </category>
        <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="84413-4"/>
            <display value="genotype display name"/>
          </coding>
        </code>
        <subject>🔗 
          <reference value="Patient/ExamplePatient"/>
        </subject>
        <effectiveDateTime value="2018"/>
        <issued value="2018-03-06T00:00:00-05:00"/>
        <performer>🔗 
          <reference value="Organization/ExampleLab"/>
        </performer>
        <valueCodeableConcept>
          <coding>
            <system value="http://www.pharmvar.org"/>
            <code value="&quot;CYP2C9"/>
            <display value="CYP2C9 *4/*35B"/>
          </coding>
        </valueCodeableConcept>
        <specimen>🔗 
          <reference value="Specimen/ExampleSpecimen"/>
        </specimen>
        <derivedFrom>
          <reference value="Observation/haplotype-1-pgx-example"/>
        </derivedFrom>
        <derivedFrom>
          <reference value="Observation/haplotype-2-pgx-example"/>
        </derivedFrom>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48018-6"/>
              <display value="Gene studied ID"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.genenames.org"/>
              <code value="HGNC:2623"/>
              <display value="CYP2C9"/>
            </coding>
          </valueCodeableConcept>
        </component>
      </Observation>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl
             value="http://example.org/fhir/Observation/haplotype-1-pgx-example"/>
    <resource>
      <Observation>
        <id value="haplotype-1-pgx-example"/>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_haplotype-1-pgx-example"> </a><p class="res-header-id"><b>Generated Narrative: Observation haplotype-1-pgx-example</b></p><a name="haplotype-1-pgx-example"> </a><a name="hchaplotype-1-pgx-example"> </a><a name="hchaplotype-1-pgx-example-en-US"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://loinc.org 84414-2}">Haplotype Name</span></p><p><b>subject</b>: <a href="Patient-ExamplePatient.html">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href="Organization-ExampleLab.html">Organization Some lab</a></p><p><b>value</b>: <span title="Codes:{http://www.pharmvar.org &quot;CYP2C9}">CYP2C9 *35B</span></p><p><b>specimen</b>: <a href="Specimen-ExampleSpecimen.html">Specimen</a></p><p><b>derivedFrom</b>: <a href="Bundle-bundle-pgxexample.html#Observation_variant-1-pgx-example">Bundle: type = transaction</a></p><h3>Components</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://loinc.org 48018-6}">Gene studied ID</span></td><td><span title="Codes:{http://www.genenames.org HGNC:2623}">CYP2C9</span></td></tr></table></div>
        </text>
        <status value="final"/>
        <category>
          <coding>
            <system
                    value="http://terminology.hl7.org/CodeSystem/observation-category"/>
            <code value="laboratory"/>
          </coding>
        </category>
        <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="84414-2"/>
            <display value="Haplotype Name"/>
          </coding>
        </code>
        <subject>🔗 
          <reference value="Patient/ExamplePatient"/>
        </subject>
        <effectiveDateTime value="2018"/>
        <issued value="2018-03-06T00:00:00-05:00"/>
        <performer>🔗 
          <reference value="Organization/ExampleLab"/>
        </performer>
        <valueCodeableConcept>
          <coding>
            <system value="http://www.pharmvar.org"/>
            <code value="&quot;CYP2C9"/>
            <display value="CYP2C9 *35B"/>
          </coding>
        </valueCodeableConcept>
        <specimen>🔗 
          <reference value="Specimen/ExampleSpecimen"/>
        </specimen>
        <derivedFrom>
          <reference value="Observation/variant-1-pgx-example"/>
        </derivedFrom>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48018-6"/>
              <display value="Gene studied ID"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.genenames.org"/>
              <code value="HGNC:2623"/>
              <display value="CYP2C9"/>
            </coding>
          </valueCodeableConcept>
        </component>
      </Observation>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl
             value="http://example.org/fhir/Observation/haplotype-2-pgx-example"/>
    <resource>
      <Observation>
        <id value="haplotype-2-pgx-example"/>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_haplotype-2-pgx-example"> </a><p class="res-header-id"><b>Generated Narrative: Observation haplotype-2-pgx-example</b></p><a name="haplotype-2-pgx-example"> </a><a name="hchaplotype-2-pgx-example"> </a><a name="hchaplotype-2-pgx-example-en-US"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://loinc.org 84414-2}">Haplotype Name</span></p><p><b>subject</b>: <a href="Patient-ExamplePatient.html">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href="Organization-ExampleLab.html">Organization Some lab</a></p><p><b>value</b>: <span title="Codes:{http://www.pharmvar.org &quot;CYP2C9}">CYP2C9 *4</span></p><p><b>specimen</b>: <a href="Specimen-ExampleSpecimen.html">Specimen</a></p><p><b>derivedFrom</b>: <a href="Bundle-bundle-pgxexample.html#Observation_variant-2-pgx-example">Bundle: type = transaction</a></p><h3>Components</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://loinc.org 48018-6}">Gene studied ID</span></td><td><span title="Codes:{http://www.genenames.org HGNC:2623}">CYP2C9</span></td></tr></table></div>
        </text>
        <status value="final"/>
        <category>
          <coding>
            <system
                    value="http://terminology.hl7.org/CodeSystem/observation-category"/>
            <code value="laboratory"/>
          </coding>
        </category>
        <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="84414-2"/>
            <display value="Haplotype Name"/>
          </coding>
        </code>
        <subject>🔗 
          <reference value="Patient/ExamplePatient"/>
        </subject>
        <effectiveDateTime value="2018"/>
        <issued value="2018-03-06T00:00:00-05:00"/>
        <performer>🔗 
          <reference value="Organization/ExampleLab"/>
        </performer>
        <valueCodeableConcept>
          <coding>
            <system value="http://www.pharmvar.org"/>
            <code value="&quot;CYP2C9"/>
            <display value="CYP2C9 *4"/>
          </coding>
        </valueCodeableConcept>
        <specimen>🔗 
          <reference value="Specimen/ExampleSpecimen"/>
        </specimen>
        <derivedFrom>
          <reference value="Observation/variant-2-pgx-example"/>
        </derivedFrom>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48018-6"/>
              <display value="Gene studied ID"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.genenames.org"/>
              <code value="HGNC:2623"/>
              <display value="CYP2C9"/>
            </coding>
          </valueCodeableConcept>
        </component>
      </Observation>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl
             value="http://example.org/fhir/Observation/variant-1-pgx-example"/>
    <resource>
      <Observation>
        <id value="variant-1-pgx-example"/>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_variant-1-pgx-example"> </a><p class="res-header-id"><b>Generated Narrative: Observation variant-1-pgx-example</b></p><a name="variant-1-pgx-example"> </a><a name="hcvariant-1-pgx-example"> </a><a name="hcvariant-1-pgx-example-en-US"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>subject</b>: <a href="Patient-ExamplePatient.html">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href="Organization-ExampleLab.html">Organization Some lab</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>specimen</b>: <a href="Specimen-ExampleSpecimen.html">Specimen</a></p><p><b>derivedFrom</b>: <a href="Bundle-bundle-pgxexample.html#MolecularSequence_sequence-1-pgx-example">Bundle: type = transaction</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48018-6}">Gene studied ID</span></p><p><b>value</b>: <span title="Codes:{http://www.genenames.org HGNC:2623}">CYP2C9</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81252-9}">Discrete genetic variant</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/projects/SNP rs12345}">rs12345</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Ref nucleotide</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69551-0}">Alt allele</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81254-5}">Genomic allele start-end</span></p><p><b>value</b>: 55227976-55227977</p></blockquote></div>
        </text>
        <status value="final"/>
        <category>
          <coding>
            <system
                    value="http://terminology.hl7.org/CodeSystem/observation-category"/>
            <code value="laboratory"/>
          </coding>
        </category>
        <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="69548-6"/>
            <display value="Genetic variant assessment"/>
          </coding>
        </code>
        <subject>🔗 
          <reference value="Patient/ExamplePatient"/>
        </subject>
        <effectiveDateTime value="2018"/>
        <issued value="2018-03-06T00:00:00-05:00"/>
        <performer>🔗 
          <reference value="Organization/ExampleLab"/>
        </performer>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA9633-4"/>
            <display value="Present"/>
          </coding>
        </valueCodeableConcept>
        <specimen>🔗 
          <reference value="Specimen/ExampleSpecimen"/>
        </specimen>
        <derivedFrom>
          <reference value="MolecularSequence/sequence-1-pgx-example"/>
        </derivedFrom>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48018-6"/>
              <display value="Gene studied ID"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.genenames.org"/>
              <code value="HGNC:2623"/>
              <display value="CYP2C9"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="81252-9"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.ncbi.nlm.nih.gov/projects/SNP"/>
              <code value="rs12345"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="69547-8"/>
              <display value="Ref nucleotide"/>
            </coding>
          </code>
          <valueString value="T"/>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="69551-0"/>
              <display value="Alt allele"/>
            </coding>
          </code>
          <valueString value="G"/>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="81254-5"/>
            </coding>
          </code>
          <valueRange>
            <low>
              <value value="55227976"/>
            </low>
            <high>
              <value value="55227977"/>
            </high>
          </valueRange>
        </component>
      </Observation>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl
             value="http://example.org/fhir/Observation/variant-2-pgx-example"/>
    <resource>
      <Observation>
        <id value="variant-2-pgx-example"/>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_variant-2-pgx-example"> </a><p class="res-header-id"><b>Generated Narrative: Observation variant-2-pgx-example</b></p><a name="variant-2-pgx-example"> </a><a name="hcvariant-2-pgx-example"> </a><a name="hcvariant-2-pgx-example-en-US"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>subject</b>: <a href="Patient-ExamplePatient.html">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href="Organization-ExampleLab.html">Organization Some lab</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>specimen</b>: <a href="Specimen-ExampleSpecimen.html">Specimen</a></p><p><b>derivedFrom</b>: <a href="Bundle-bundle-pgxexample.html#MolecularSequence_sequence-2-pgx-example">Bundle: type = transaction</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48018-6}">Gene studied ID</span></p><p><b>value</b>: <span title="Codes:{http://www.genenames.org HGNC:2623}">CYP2C9</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48013-7}">Genomic reference sequence ID</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NG_007726.3}">NG_007726.3</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81252-9}">Discrete genetic variant</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/projects/SNP rs233455}">rs233455</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Ref nucleotide</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69551-0}">Alt allele</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81254-5}">Genomic allele start-end</span></p><p><b>value</b>: 55227978-55227979</p></blockquote></div>
        </text>
        <status value="final"/>
        <category>
          <coding>
            <system
                    value="http://terminology.hl7.org/CodeSystem/observation-category"/>
            <code value="laboratory"/>
          </coding>
        </category>
        <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="69548-6"/>
            <display value="Genetic variant assessment"/>
          </coding>
        </code>
        <subject>🔗 
          <reference value="Patient/ExamplePatient"/>
        </subject>
        <effectiveDateTime value="2018"/>
        <issued value="2018-03-06T00:00:00-05:00"/>
        <performer>🔗 
          <reference value="Organization/ExampleLab"/>
        </performer>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA9633-4"/>
            <display value="Present"/>
          </coding>
        </valueCodeableConcept>
        <specimen>🔗 
          <reference value="Specimen/ExampleSpecimen"/>
        </specimen>
        <derivedFrom>
          <reference value="MolecularSequence/sequence-2-pgx-example"/>
        </derivedFrom>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48018-6"/>
              <display value="Gene studied ID"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.genenames.org"/>
              <code value="HGNC:2623"/>
              <display value="CYP2C9"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48013-7"/>
              <display value="Genomic reference sequence ID"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
              <code value="NG_007726.3"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="81252-9"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.ncbi.nlm.nih.gov/projects/SNP"/>
              <code value="rs233455"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="69547-8"/>
              <display value="Ref nucleotide"/>
            </coding>
          </code>
          <valueString value="T"/>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="69551-0"/>
              <display value="Alt allele"/>
            </coding>
          </code>
          <valueString value="G"/>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="81254-5"/>
            </coding>
          </code>
          <valueRange>
            <low>
              <value value="55227978"/>
            </low>
            <high>
              <value value="55227979"/>
            </high>
          </valueRange>
        </component>
      </Observation>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl
             value="http://example.org/fhir/MolecularSequence/sequence-1-pgx-example"/>
    <resource>
      <MolecularSequence>
        <id value="sequence-1-pgx-example"/>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="MolecularSequence_sequence-1-pgx-example"> </a><p class="res-header-id"><b>Generated Narrative: MolecularSequence sequence-1-pgx-example</b></p><a name="sequence-1-pgx-example"> </a><a name="hcsequence-1-pgx-example"> </a><a name="hcsequence-1-pgx-example-en-US"> </a><p><b>type</b>: DNA Sequence</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td style="display: none">*</td><td>Sense orientation of referenceSeq</td><td><span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NG-007726.3}">NG-007726.3</span></td><td>55227970</td><td>55227980</td></tr></table></div>
        </text>
        <type value="dna"/>
        <coordinateSystem value="0"/>
        <referenceSeq>
          <orientation value="sense"/>
          <referenceSeqId>
            <coding>
              <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
              <code value="NG-007726.3"/>
            </coding>
          </referenceSeqId>
          <windowStart value="55227970"/>
          <windowEnd value="55227980"/>
        </referenceSeq>
      </MolecularSequence>
    </resource>
    <request>
      <method value="POST"/>
      <url value="MolecularSequence"/>
    </request>
  </entry>
  <entry>
    <fullUrl
             value="http://example.org/fhir/MolecularSequence/sequence-2-pgx-example"/>
    <resource>
      <MolecularSequence>
        <id value="sequence-2-pgx-example"/>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="MolecularSequence_sequence-2-pgx-example"> </a><p class="res-header-id"><b>Generated Narrative: MolecularSequence sequence-2-pgx-example</b></p><a name="sequence-2-pgx-example"> </a><a name="hcsequence-2-pgx-example"> </a><a name="hcsequence-2-pgx-example-en-US"> </a><p><b>type</b>: DNA Sequence</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td style="display: none">*</td><td>Sense orientation of referenceSeq</td><td><span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NG-007726.3}">NG-007726.3</span></td><td>55227970</td><td>55227980</td></tr></table></div>
        </text>
        <type value="dna"/>
        <coordinateSystem value="0"/>
        <referenceSeq>
          <orientation value="sense"/>
          <referenceSeqId>
            <coding>
              <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
              <code value="NG-007726.3"/>
            </coding>
          </referenceSeqId>
          <windowStart value="55227970"/>
          <windowEnd value="55227980"/>
        </referenceSeq>
      </MolecularSequence>
    </resource>
    <request>
      <method value="POST"/>
      <url value="MolecularSequence"/>
    </request>
  </entry>
  <entry>
    <fullUrl
             value="http://example.org/fhir/Task/med-usage-impact-task-pgx-example"/>
    <resource>
      <Task>
        <id value="med-usage-impact-task-pgx-example"/>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-recommendation"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Task_med-usage-impact-task-pgx-example"> </a><p class="res-header-id"><b>Generated Narrative: Task med-usage-impact-task-pgx-example</b></p><a name="med-usage-impact-task-pgx-example"> </a><a name="hcmed-usage-impact-task-pgx-example"> </a><a name="hcmed-usage-impact-task-pgx-example-en-US"> </a><p><b>status</b>: Requested</p><p><b>intent</b>: proposal</p><p><b>code</b>: <span title="Codes:{http://loinc.org LA26423-6}">Any Increase does Recommendation Text from the provider</span></p><p><b>description</b>: Any Increase does Recommendation Text from the provider</p><p><b>focus</b>: <a href="Bundle-bundle-pgxexample.html#MedicationStatement_current-med-example">Bundle: type = transaction</a></p><p><b>for</b>: <a href="Patient-ExamplePatient.html">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>reasonReference</b>: <a href="Bundle-bundle-pgxexample.html#Observation_med-impact-pgx-example">Bundle: type = transaction</a></p></div>
        </text>
        <status value="requested"/>
        <intent value="proposal"/>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA26423-6"/>
            <display value="Increase dose"/>
          </coding>
          <text
                value="Any Increase does Recommendation Text from the provider"/>
        </code>
        <description
                     value="Any Increase does Recommendation Text from the provider"/>
        <focus>
          <reference value="MedicationStatement/current-med-example"/>
        </focus>
        <for>🔗 
          <reference value="Patient/ExamplePatient"/>
        </for>
        <reasonReference>
          <reference value="Observation/med-impact-pgx-example"/>
        </reasonReference>
      </Task>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Task"/>
    </request>
  </entry>
  <entry>
    <fullUrl
             value="http://example.org/fhir/MedicationStatement/current-med-example"/>
    <resource>
      <MedicationStatement>
        <id value="current-med-example"/>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="MedicationStatement_current-med-example"> </a><p class="res-header-id"><b>Generated Narrative: MedicationStatement current-med-example</b></p><a name="current-med-example"> </a><a name="hccurrent-med-example"> </a><a name="hccurrent-med-example-en-US"> </a><p><b>status</b>: Unknown</p><p><b>medication</b>: <span title="Codes:{http://www.nlm.nih.gov/research/umls/rxnorm 103}">mercaptopurine</span></p><p><b>subject</b>: <a href="Patient-ExamplePatient.html">Anonymous Patient (no stated gender), DoB Unknown</a></p></div>
        </text>
        <status value="unknown"/>
        <medicationCodeableConcept>
          <coding>
            <system value="http://www.nlm.nih.gov/research/umls/rxnorm"/>
            <code value="103"/>
            <display value="mercaptopurine"/>
          </coding>
        </medicationCodeableConcept>
        <subject>🔗 
          <reference value="Patient/ExamplePatient"/>
        </subject>
      </MedicationStatement>
    </resource>
    <request>
      <method value="POST"/>
      <url value="MedicationStatement"/>
    </request>
  </entry>
</Bundle>