Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild 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><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"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-genomic-report.html">Genomic Report</a></p></div><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>Anonymous Patient (no stated gender), DoB Unknown</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><td><b>Flags</b></td><td><b>When For</b></td></tr><tr><td><a href="Bundle-bundle-pgxexample.html#Observation_med-impact-pgx-example"><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>2018</td></tr><tr><td><a href="Bundle-bundle-pgxexample.html#Observation_genotype-pgx-example"><span title="Codes:{http://loinc.org 84413-4}">genotype display name</span></a></td><td><span title="Codes:{http://www.pharmvar.org CYP2C9}">CYP2C9 *4/*35B</span></td><td>Final</td><td>2018</td></tr><tr><td><a href="Bundle-bundle-pgxexample.html#Observation_haplotype-1-pgx-example"><span title="Codes:{http://loinc.org 84414-2}">Haplotype Name</span></a></td><td><span title="Codes:{http://www.pharmvar.org CYP2C9}">CYP2C9 *35B</span></td><td>Final</td><td>2018</td></tr><tr><td><a href="Bundle-bundle-pgxexample.html#Observation_haplotype-2-pgx-example"><span title="Codes:{http://loinc.org 84414-2}">Haplotype Name</span></a></td><td><span title="Codes:{http://www.pharmvar.org CYP2C9}">CYP2C9 *4</span></td><td>Final</td><td>2018</td></tr><tr><td><a href="Bundle-bundle-pgxexample.html#Observation_variant-1-pgx-example"><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>2018</td></tr><tr><td><a href="Bundle-bundle-pgxexample.html#Observation_variant-2-pgx-example"><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>2018</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"><a name="Patient_ExamplePatient"> </a>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><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><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><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><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"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-therapeutic-implication.html">Therapeutic Implication</a></p></div><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">Observation genotype display name</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><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"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-genotype.html">Genotype</a></p></div><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 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">Observation Haplotype Name</a></li><li><a href="Bundle-bundle-pgxexample.html#Observation_haplotype-2-pgx-example">Observation Haplotype Name</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="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><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"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-haplotype.html">Haplotype</a></p></div><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 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">Observation Genetic variant assessment</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="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><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"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-haplotype.html">Haplotype</a></p></div><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 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">Observation Genetic variant assessment</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="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><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"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-variant.html">Variant</a></p></div><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">MolecularSequence: type = dna; coordinateSystem = 0</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><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"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-variant.html">Variant</a></p></div><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">MolecularSequence: type = dna; coordinateSystem = 0</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><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><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><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"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-medication-recommendation.html">Medication Recommendation</a></p></div><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">MedicationStatement: status = unknown; medication[x] = mercaptopurine</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">Observation Therapeutic Implication</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><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>