bundle-oncology-report-example - XML Representation - Genomics Reporting Implementation Guide v3.0.0

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions
: bundle-oncology-report-example - XML Representation

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<Bundle xmlns="http://hl7.org/fhir">
  <id value="bundle-oncology-report-example"/>
  <type value="transaction"/>
  <entry>
    <fullUrl value="urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17"/>
    <resource>
      <Organization>
        <id value="Inline-Instance-for-oncology-report-example-1"/>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Organization_Inline-Instance-for-oncology-report-example-1"> </a><p class="res-header-id"><b>Generated Narrative: Organization Inline-Instance-for-oncology-report-example-1</b></p><a name="Inline-Instance-for-oncology-report-example-1"> </a><a name="hcInline-Instance-for-oncology-report-example-1"> </a><a name="Inline-Instance-for-oncology-report-example-1-en-US"> </a><p><b>identifier</b>: <code>http://molit.eu/fhir/genomics/NamingSystem/organization</code>/CEGAT</p><p><b>name</b>: CEGAT</p></div>
        </text>
        <identifier>
          <system
                  value="http://molit.eu/fhir/genomics/NamingSystem/organization"/>
          <value value="CEGAT"/>
        </identifier>
        <name value="CEGAT"/>
      </Organization>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Organization"/>
      <ifNoneExist
                   value="identifier=http://molit.eu/fhir/genomics/NamingSystem/organization|CEGAT"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648"/>
    <resource>
      <Patient>
        <id value="Inline-Instance-for-oncology-report-example-2"/>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Patient_Inline-Instance-for-oncology-report-example-2"> </a><p class="res-header-id"><b>Generated Narrative: Patient Inline-Instance-for-oncology-report-example-2</b></p><a name="Inline-Instance-for-oncology-report-example-2"> </a><a name="hcInline-Instance-for-oncology-report-example-2"> </a><a name="Inline-Instance-for-oncology-report-example-2-en-US"> </a><p style="border: 1px #661aff solid; background-color: #e6e6ff; padding: 10px;">Anonymous Patient (no stated gender), DoB Unknown ( http://molit.eu/fhir/genomics/NamingSystem/cegat/patID#11111)</p><hr/></div>
        </text>
        <identifier>
          <system
                  value="http://molit.eu/fhir/genomics/NamingSystem/cegat/patID"/>
          <value value="11111"/>
        </identifier>
      </Patient>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Patient"/>
      <ifNoneExist
                   value="identifier=http://molit.eu/fhir/genomics/NamingSystem/cegat/patID|11111"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="urn:uuid:a2041c83-b73d-4fc8-9466-4ba4a92da516"/>
    <resource>
      <Specimen>
        <id value="Inline-Instance-for-oncology-report-example-3"/>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Specimen_Inline-Instance-for-oncology-report-example-3"> </a><p class="res-header-id"><b>Generated Narrative: Specimen Inline-Instance-for-oncology-report-example-3</b></p><a name="Inline-Instance-for-oncology-report-example-3"> </a><a name="hcInline-Instance-for-oncology-report-example-3"> </a><a name="Inline-Instance-for-oncology-report-example-3-en-US"> </a><p><b>identifier</b>: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><p><b>type</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0487 TUMOR}">Tumor</span></p><p><b>subject</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><h3>Collections</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Method</b></td><td><b>BodySite</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:">Biopsy</span></td><td><span title="Codes:{http://hl7.org/fhir/sid/icd-10-cm C16.0}">Malignant neoplasm of cardia</span></td></tr></table></div>
        </text>
        <identifier>
          <system
                  value="http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID"/>
          <value value="UNKNOWN"/>
        </identifier>
        <type>
          <coding>
            <system value="http://terminology.hl7.org/CodeSystem/v2-0487"/>
            <code value="TUMOR"/>
            <display value="Tumor"/>
          </coding>
        </type>
        <subject>
          <reference value="urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648"/>
        </subject>
        <collection>
          <method>
            <text value="Biopsy"/>
          </method>
          <bodySite>
            <coding>
              <system value="http://hl7.org/fhir/sid/icd-10-cm"/>
              <code value="C16.0"/>
            </coding>
          </bodySite>
        </collection>
      </Specimen>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Specimen"/>
      <ifNoneExist
                   value="identifier=http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID|UNKNOWN"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="urn:uuid:dac358c3-403a-4dbb-b478-4259aed882ae"/>
    <resource>
      <Observation>
        <id value="Inline-Instance-for-oncology-report-example-4"/>
        <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_Inline-Instance-for-oncology-report-example-4"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-4</b></p><a name="Inline-Instance-for-oncology-report-example-4"> </a><a name="hcInline-Instance-for-oncology-report-example-4"> </a><a name="Inline-Instance-for-oncology-report-example-4-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="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><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:8975}">PIK3CA</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_006218.4:c.3140A&gt;G}">NM_006218.4:c.3140A&gt;G</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:1000002}">substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48005-3}">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NP_006209.2:p.His1047Arg}">NP_006209.2:p.His1047Arg</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_006218.3}">NM_006218.4</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</span></p><p><b>value</b>: A</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.2188 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 64 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</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://loinc.org"/>
            <code value="69548-6"/>
            <display value="Genetic variant assessment"/>
          </coding>
        </code>
        <subject>
          <reference value="urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648"/>
        </subject>
        <effectiveDateTime value="2023-03-05"/>
        <performer>
          <reference value="urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17"/>
        </performer>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA9633-4"/>
            <display value="Present"/>
          </coding>
        </valueCodeableConcept>
        <method>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA26398-0"/>
            <display value="Sequencing"/>
          </coding>
        </method>
        <specimen>
          <identifier>
            <system
                    value="http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID"/>
            <value value="UNKNOWN"/>
          </identifier>
        </specimen>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48002-0"/>
              <display value="Genomic source class"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://loinc.org"/>
              <code value="LA6684-0"/>
              <display value="Somatic"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <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:8975"/>
              <display value="PIK3CA"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="62374-4"/>
              <display value="Human reference sequence assembly version"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://loinc.org"/>
              <code value="LA14029-5"/>
              <display value="GRCh37"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48004-6"/>
              <display value="DNA change (c.HGVS)"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://varnomen.hgvs.org"/>
              <code value="NM_006218.4:c.3140A&gt;G"/>
              <display value="NM_006218.4:c.3140A&gt;G"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48019-4"/>
              <display value="DNA change type"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.sequenceontology.org"/>
              <code value="SO:1000002"/>
              <display value="substitution"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48005-3"/>
              <display value="Amino acid change (pHGVS)"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://varnomen.hgvs.org"/>
              <code value="NP_006209.2:p.His1047Arg"/>
              <display value="NP_006209.2:p.His1047Arg"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="51958-7"/>
              <display value="Transcript reference sequence [ID]"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
              <code value="NM_006218.3"/>
              <display value="NM_006218.4"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="69547-8"/>
              <display value="Genomic ref allele [ID]"/>
            </coding>
          </code>
          <valueString value="A"/>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="81258-6"/>
              <display value="Sample VAF"/>
            </coding>
          </code>
          <valueQuantity>
            <value value="0.2188"/>
            <unit
                  value="relative frequency of a particular allele in the specimen"/>
            <system value="http://unitsofmeasure.org"/>
            <code value="1"/>
          </valueQuantity>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="82121-5"/>
              <display value="Allelic read depth"/>
            </coding>
          </code>
          <valueQuantity>
            <value value="64"/>
            <unit value="reads per base pair"/>
            <system value="http://unitsofmeasure.org"/>
            <code value="1"/>
          </valueQuantity>
        </component>
      </Observation>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="urn:uuid:1d773d66-cec7-44a2-b92a-46d00adeae00"/>
    <resource>
      <Observation>
        <id value="Inline-Instance-for-oncology-report-example-5"/>
        <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_Inline-Instance-for-oncology-report-example-5"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-5</b></p><a name="Inline-Instance-for-oncology-report-example-5"> </a><a name="hcInline-Instance-for-oncology-report-example-5"> </a><a name="Inline-Instance-for-oncology-report-example-5-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="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><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:7989}">NRAS</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_002524.4:c.34G&gt;T}">NM_002524.4:c.34G&gt;T</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:1000002}">substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_002524.4}">NM_002524.4</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.1793 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 145 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</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://loinc.org"/>
            <code value="69548-6"/>
            <display value="Genetic variant assessment"/>
          </coding>
        </code>
        <subject>
          <reference value="urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648"/>
        </subject>
        <effectiveDateTime value="2023-03-05"/>
        <performer>
          <reference value="urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17"/>
        </performer>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA9633-4"/>
            <display value="Present"/>
          </coding>
        </valueCodeableConcept>
        <method>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA26398-0"/>
            <display value="Sequencing"/>
          </coding>
        </method>
        <specimen>
          <identifier>
            <system
                    value="http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID"/>
            <value value="UNKNOWN"/>
          </identifier>
        </specimen>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48002-0"/>
              <display value="Genomic source class"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://loinc.org"/>
              <code value="LA6684-0"/>
              <display value="Somatic"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <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:7989"/>
              <display value="NRAS"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="62374-4"/>
              <display value="Human reference sequence assembly version"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://loinc.org"/>
              <code value="LA14029-5"/>
              <display value="GRCh37"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48004-6"/>
              <display value="DNA change (c.HGVS)"/>
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        <component>
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              <display value="Sample VAF"/>
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          <valueQuantity>
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            <unit
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            <system value="http://unitsofmeasure.org"/>
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        <component>
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              <code value="82121-5"/>
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            <unit value="reads per base pair"/>
            <system value="http://unitsofmeasure.org"/>
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  <entry>
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        <meta>
          <profile
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        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncology-report-example-6"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-6</b></p><a name="Inline-Instance-for-oncology-report-example-6"> </a><a name="hcInline-Instance-for-oncology-report-example-6"> </a><a name="Inline-Instance-for-oncology-report-example-6-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="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><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:16712}">FBXW7</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_001349798.2:c.1394G&gt;A}">NM_001349798.2:c.1394G&gt;A</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:1000002}">substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48005-3}">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NP_001336727.1:p.Arg465His}">NP_001336727.1:p.Arg465His</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_001349798.2}">NM_001349798.2</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.1053 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 57 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote></div>
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        <subject>
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        <performer>
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        <valueCodeableConcept>
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            <display value="Present"/>
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        <method>
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            <system value="http://loinc.org"/>
            <code value="LA26398-0"/>
            <display value="Sequencing"/>
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        </method>
        <specimen>
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            <system
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        <component>
          <code>
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              <code value="48002-0"/>
              <display value="Genomic source class"/>
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          <valueCodeableConcept>
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        <component>
          <code>
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              <code value="48018-6"/>
              <display value="Gene studied [ID]"/>
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        <component>
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              <display value="Amino acid change (pHGVS)"/>
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        <component>
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              <code value="51958-7"/>
              <display value="Transcript reference sequence [ID]"/>
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          <valueCodeableConcept>
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              <display value="NM_001349798.2"/>
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        <component>
          <code>
            <coding>
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              <code value="69547-8"/>
              <display value="Genomic ref allele [ID]"/>
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        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="81258-6"/>
              <display value="Sample VAF"/>
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            <unit
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            <system value="http://unitsofmeasure.org"/>
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        <component>
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              <code value="82121-5"/>
              <display value="Allelic read depth"/>
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            <unit value="reads per base pair"/>
            <system value="http://unitsofmeasure.org"/>
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    <resource>
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        <meta>
          <profile
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        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncology-report-example-7"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-7</b></p><a name="Inline-Instance-for-oncology-report-example-7"> </a><a name="hcInline-Instance-for-oncology-report-example-7"> </a><a name="Inline-Instance-for-oncology-report-example-7-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="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><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:7133}">KMT2D</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_003482.3:c.7900_7901delCA}">NM_003482.3:c.7900_7901delCA</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:0000159}">deletion</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_003482.3}">NM_003482.3</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</span></p><p><b>value</b>: CTG</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.188 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 117 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote></div>
        </text>
        <status value="final"/>
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            <code value="GE"/>
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        <code>
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            <code value="69548-6"/>
            <display value="Genetic variant assessment"/>
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        <effectiveDateTime value="2023-03-05"/>
        <performer>
          <reference value="urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17"/>
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            <system value="http://loinc.org"/>
            <code value="LA9633-4"/>
            <display value="Present"/>
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        <method>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA26398-0"/>
            <display value="Sequencing"/>
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        </method>
        <specimen>
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            <system
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            <value value="UNKNOWN"/>
          </identifier>
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        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48002-0"/>
              <display value="Genomic source class"/>
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          </code>
          <valueCodeableConcept>
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              <system value="http://loinc.org"/>
              <code value="LA6684-0"/>
              <display value="Somatic"/>
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          </valueCodeableConcept>
        </component>
        <component>
          <code>
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              <code value="48018-6"/>
              <display value="Gene studied [ID]"/>
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          </code>
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              <display value="KMT2D"/>
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              <code value="62374-4"/>
              <display value="Human reference sequence assembly version"/>
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        <component>
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              <display value="NM_003482.3:c.7900_7901delCA"/>
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        <component>
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        <component>
          <code>
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              <code value="51958-7"/>
              <display value="Transcript reference sequence [ID]"/>
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          <valueCodeableConcept>
            <coding>
              <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
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              <display value="NM_003482.3"/>
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          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="69547-8"/>
              <display value="Genomic ref allele [ID]"/>
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          <valueString value="CTG"/>
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        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="81258-6"/>
              <display value="Sample VAF"/>
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          </code>
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            <unit
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            <system value="http://unitsofmeasure.org"/>
            <code value="1"/>
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        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="82121-5"/>
              <display value="Allelic read depth"/>
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          <valueQuantity>
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            <unit value="reads per base pair"/>
            <system value="http://unitsofmeasure.org"/>
            <code value="1"/>
          </valueQuantity>
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    <request>
      <method value="POST"/>
      <url value="Observation"/>
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  </entry>
  <entry>
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    <resource>
      <Observation>
        <id value="Inline-Instance-for-oncology-report-example-8"/>
        <meta>
          <profile
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        </meta>
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          <status value="generated"/>
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          <code>
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              <display value="Sample VAF"/>
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            <unit
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            <system value="http://unitsofmeasure.org"/>
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            <unit value="reads per base pair"/>
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          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncology-report-example-9"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-9</b></p><a name="Inline-Instance-for-oncology-report-example-9"> </a><a name="hcInline-Instance-for-oncology-report-example-9"> </a><a name="Inline-Instance-for-oncology-report-example-9-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="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><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:6126}">IRS2</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_003749.2:c.3960C&gt;T}">NM_003749.2:c.3960C&gt;T</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:1000002}">substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_003749.2}">NM_003749.2</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</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 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.1343 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 134 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote></div>
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              <system value="http://loinc.org"/>
              <code value="48002-0"/>
              <display value="Genomic source class"/>
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        <component>
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          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncology-report-example-10"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-10</b></p><a name="Inline-Instance-for-oncology-report-example-10"> </a><a name="hcInline-Instance-for-oncology-report-example-10"> </a><a name="Inline-Instance-for-oncology-report-example-10-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="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><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:1787}">CDKN2A</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_000077.4:c.9_32del}">NM_000077.4:c.9_32del</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:0000159}">deletion</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48005-3}">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NP_000068.1:p.Ala4_Pro11del}">NP_000068.1:p.Ala4_Pro11del</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_000077.4}">NM_000077.4</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</span></p><p><b>value</b>: AGGCTCCATGCTGCTCCCCGCCGCC</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.0536 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 112 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote></div>
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            <system value="http://loinc.org"/>
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          <code>
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              <code value="48002-0"/>
              <display value="Genomic source class"/>
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          </code>
          <valueCodeableConcept>
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              <system value="http://loinc.org"/>
              <code value="LA6684-0"/>
              <display value="Somatic"/>
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        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48018-6"/>
              <display value="Gene studied [ID]"/>
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          <valueCodeableConcept>
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          <valueCodeableConcept>
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              <code value="51958-7"/>
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          <valueCodeableConcept>
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              <display value="NM_000077.4"/>
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        <component>
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              <system value="http://loinc.org"/>
              <code value="69547-8"/>
              <display value="Genomic ref allele [ID]"/>
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        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="81258-6"/>
              <display value="Sample VAF"/>
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          </code>
          <valueQuantity>
            <value value="0.0536"/>
            <unit
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            <system value="http://unitsofmeasure.org"/>
            <code value="1"/>
          </valueQuantity>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="82121-5"/>
              <display value="Allelic read depth"/>
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          </code>
          <valueQuantity>
            <value value="112"/>
            <unit value="reads per base pair"/>
            <system value="http://unitsofmeasure.org"/>
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        <meta>
          <profile
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        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncology-report-example-11"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-11</b></p><a name="Inline-Instance-for-oncology-report-example-11"> </a><a name="hcInline-Instance-for-oncology-report-example-11"> </a><a name="Inline-Instance-for-oncology-report-example-11-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="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><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:9949}">RECQL4</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_004260.4:c.2086C&gt;T}">NM_004260.4:c.2086C&gt;T</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:1000002}">substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48005-3}">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NP_004251.4:p.Arg696Cys}">NP_004251.4:p.Arg696Cys</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_004260.4}">NM_004260.4</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</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 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.2568 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 148 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote></div>
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        <code>
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            <code value="69548-6"/>
            <display value="Genetic variant assessment"/>
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        <performer>
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        <valueCodeableConcept>
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            <system value="http://loinc.org"/>
            <code value="LA9633-4"/>
            <display value="Present"/>
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        <method>
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            <system value="http://loinc.org"/>
            <code value="LA26398-0"/>
            <display value="Sequencing"/>
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        </method>
        <specimen>
          <identifier>
            <system
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            <value value="UNKNOWN"/>
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        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48002-0"/>
              <display value="Genomic source class"/>
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          </code>
          <valueCodeableConcept>
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              <system value="http://loinc.org"/>
              <code value="LA6684-0"/>
              <display value="Somatic"/>
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          </valueCodeableConcept>
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        <component>
          <code>
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              <code value="48018-6"/>
              <display value="Gene studied [ID]"/>
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            <unit
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              <code value="82121-5"/>
              <display value="Allelic read depth"/>
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            <unit value="reads per base pair"/>
            <system value="http://unitsofmeasure.org"/>
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          <profile
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        </meta>
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          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncology-report-example-12"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-12</b></p><a name="Inline-Instance-for-oncology-report-example-12"> </a><a name="hcInline-Instance-for-oncology-report-example-12"> </a><a name="Inline-Instance-for-oncology-report-example-12-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="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><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:10483}">RYR1</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_000540.3:c.4964G&gt;A}">NM_000540.3:c.4964G&gt;A</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:1000002}">substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48005-3}">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NP_000531.2:p.Arg1655Leu}">NP_000531.2:p.Arg1655Leu</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_000540.2}">NM_000540.3</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</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 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.2151 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 93 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote></div>
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        <component>
          <code>
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              <display value="NM_000540.3"/>
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              <code value="81258-6"/>
              <display value="Sample VAF"/>
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            <unit
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            <system value="http://unitsofmeasure.org"/>
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        <component>
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            <coding>
              <system value="http://loinc.org"/>
              <code value="82121-5"/>
              <display value="Allelic read depth"/>
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            <unit value="reads per base pair"/>
            <system value="http://unitsofmeasure.org"/>
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          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncology-report-example-13"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-13</b></p><a name="Inline-Instance-for-oncology-report-example-13"> </a><a name="hcInline-Instance-for-oncology-report-example-13"> </a><a name="Inline-Instance-for-oncology-report-example-13-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="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><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:10519}">SACS</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_014363.5:c.12118G&gt;A}">NM_014363.5:c.12118G&gt;A</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:1000002}">substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_014363.5}">NM_014363.5</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.3333 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 60 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote></div>
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        <method>
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            <system value="http://loinc.org"/>
            <code value="LA26398-0"/>
            <display value="Sequencing"/>
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          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48002-0"/>
              <display value="Genomic source class"/>
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          </code>
          <valueCodeableConcept>
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              <code value="LA6684-0"/>
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        <component>
          <code>
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          </code>
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        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncology-report-example-14"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-14</b></p><a name="Inline-Instance-for-oncology-report-example-14"> </a><a name="hcInline-Instance-for-oncology-report-example-14"> </a><a name="Inline-Instance-for-oncology-report-example-14-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="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><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:11086}">SLIT2</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_004787.3:c.1290C&gt;A}">NM_004787.3:c.1290C&gt;A</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:1000002}">substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_004787.3}">NM_004787.3</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.2642 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 53 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote></div>
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        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="69548-6"/>
            <display value="Genetic variant assessment"/>
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        <effectiveDateTime value="2023-03-05"/>
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            <system value="http://loinc.org"/>
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            <system value="http://loinc.org"/>
            <code value="LA26398-0"/>
            <display value="Sequencing"/>
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        <specimen>
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          <code>
            <coding>
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              <code value="48002-0"/>
              <display value="Genomic source class"/>
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          </code>
          <valueCodeableConcept>
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              <system value="http://loinc.org"/>
              <code value="LA6684-0"/>
              <display value="Somatic"/>
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        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48018-6"/>
              <display value="Gene studied [ID]"/>
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          <valueCodeableConcept>
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              <system value="http://www.genenames.org"/>
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              <display value="SLIT2"/>
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        <component>
          <code>
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              <code value="62374-4"/>
              <display value="Human reference sequence assembly version"/>
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          <valueCodeableConcept>
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              <code value="LA14029-5"/>
              <display value="GRCh37"/>
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              <display value="DNA change type"/>
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          <valueCodeableConcept>
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              <system value="http://www.sequenceontology.org"/>
              <code value="SO:1000002"/>
              <display value="substitution"/>
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        <component>
          <code>
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              <system value="http://loinc.org"/>
              <code value="51958-7"/>
              <display value="Transcript reference sequence [ID]"/>
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          <valueCodeableConcept>
            <coding>
              <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
              <code value="NM_004787.3"/>
              <display value="NM_004787.3"/>
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          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="69547-8"/>
              <display value="Genomic ref allele [ID]"/>
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          <valueString value="C"/>
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        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="81258-6"/>
              <display value="Sample VAF"/>
            </coding>
          </code>
          <valueQuantity>
            <value value="0.2642"/>
            <unit
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            <system value="http://unitsofmeasure.org"/>
            <code value="1"/>
          </valueQuantity>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="82121-5"/>
              <display value="Allelic read depth"/>
            </coding>
          </code>
          <valueQuantity>
            <value value="53"/>
            <unit value="reads per base pair"/>
            <system value="http://unitsofmeasure.org"/>
            <code value="1"/>
          </valueQuantity>
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    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="urn:uuid:1a71e80f-b044-4a91-80e1-eadbe5a53dca"/>
    <resource>
      <Observation>
        <id value="Inline-Instance-for-oncology-report-example-15"/>
        <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_Inline-Instance-for-oncology-report-example-15"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-report-example-15</b></p><a name="Inline-Instance-for-oncology-report-example-15"> </a><a name="hcInline-Instance-for-oncology-report-example-15"> </a><a name="Inline-Instance-for-oncology-report-example-15-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="Bundle-bundle-oncology-report-example.html#urn-uuid-f7a438e6-f484-453d-97e8-aa4d51008648">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-03-05</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID</code>/UNKNOWN</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6684-0}">Somatic</span></p></blockquote><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:11100}">SMARCA4</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 62374-4}">Human reference sequence assembly version</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14029-5}">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_003072.5:c.2372C&gt;T}">NM_003072.5:c.2372C&gt;T</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:1000002}">substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48005-3}">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NP_003063.2:p.Ala791Val}">NP_003063.2:p.Ala791Val</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_003072.5}">NM_003072.5</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69547-8}">Genomic ref allele [ID]</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.1938 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 82121-5}">Allelic read depth</span></p><p><b>value</b>: 160 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote></div>
        </text>
        <status value="final"/>
        <category>
          <coding>
            <system
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            <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"/>
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        </code>
        <subject>
          <reference value="urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648"/>
        </subject>
        <effectiveDateTime value="2023-03-05"/>
        <performer>
          <reference value="urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17"/>
        </performer>
        <valueCodeableConcept>
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            <system value="http://loinc.org"/>
            <code value="LA9633-4"/>
            <display value="Present"/>
          </coding>
        </valueCodeableConcept>
        <method>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA26398-0"/>
            <display value="Sequencing"/>
          </coding>
        </method>
        <specimen>
          <identifier>
            <system
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            <value value="UNKNOWN"/>
          </identifier>
        </specimen>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48002-0"/>
              <display value="Genomic source class"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://loinc.org"/>
              <code value="LA6684-0"/>
              <display value="Somatic"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <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:11100"/>
              <display value="SMARCA4"/>
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          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="62374-4"/>
              <display value="Human reference sequence assembly version"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://loinc.org"/>
              <code value="LA14029-5"/>
              <display value="GRCh37"/>
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          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48004-6"/>
              <display value="DNA change (c.HGVS)"/>
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          </code>
          <valueCodeableConcept>
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              <system value="http://varnomen.hgvs.org"/>
              <code value="NM_003072.5:c.2372C&gt;T"/>
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        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48019-4"/>
              <display value="DNA change type"/>
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          </code>
          <valueCodeableConcept>
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              <system value="http://www.sequenceontology.org"/>
              <code value="SO:1000002"/>
              <display value="substitution"/>
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        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48005-3"/>
              <display value="Amino acid change (pHGVS)"/>
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          </code>
          <valueCodeableConcept>
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              <system value="http://varnomen.hgvs.org"/>
              <code value="NP_003063.2:p.Ala791Val"/>
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              <system value="http://loinc.org"/>
              <code value="51958-7"/>
              <display value="Transcript reference sequence [ID]"/>
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          <valueCodeableConcept>
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              <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
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              <display value="NM_003072.5"/>
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          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="69547-8"/>
              <display value="Genomic ref allele [ID]"/>
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          <valueString value="C"/>
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        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="81258-6"/>
              <display value="Sample VAF"/>
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          </code>
          <valueQuantity>
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            <unit
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            <system value="http://unitsofmeasure.org"/>
            <code value="1"/>
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        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="82121-5"/>
              <display value="Allelic read depth"/>
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          </code>
          <valueQuantity>
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            <unit value="reads per base pair"/>
            <system value="http://unitsofmeasure.org"/>
            <code value="1"/>
          </valueQuantity>
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    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="urn:uuid:6a80003f-822d-489e-8286-1f1dcba56dfa"/>
    <resource>
      <DiagnosticReport>
        <id value="Inline-Instance-for-oncology-report-example-16"/>
        <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_Inline-Instance-for-oncology-report-example-16"> </a><p class="res-header-id"><b>Generated Narrative: DiagnosticReport Inline-Instance-for-oncology-report-example-16</b></p><a name="Inline-Instance-for-oncology-report-example-16"> </a><a name="hcInline-Instance-for-oncology-report-example-16"> </a><a name="Inline-Instance-for-oncology-report-example-16-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>Not done yet</td></tr><tr><td>Reported</td><td>2019-09-15 11:35:05-0400</td></tr><tr><td>Performer</td><td> <a href="Bundle-bundle-oncology-report-example.html#urn-uuid-fc16d84c-8584-4e1d-baae-64e2f95bfe17">Bundle: type = transaction</a></td></tr><tr><td>Identifier</td><td> <code>http://molit.eu/fhir/genomics/NamingSystem/cegat/reportID</code>/42867</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><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>
        <identifier>
          <system
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          <value value="42867"/>
        </identifier>
        <status value="final"/>
        <category>
          <coding>
            <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
            <code value="GE"/>
          </coding>
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        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="51969-4"/>
            <display value="Genetic analysis report"/>
          </coding>
        </code>
        <subject>
          <reference value="urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648"/>
        </subject>
        <issued value="2019-09-15T11:35:05.722-04:00"/>
        <performer>
          <reference value="urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17"/>
        </performer>
        <specimen>
          <reference value="urn:uuid:a2041c83-b73d-4fc8-9466-4ba4a92da516"/>
        </specimen>
        <result>
          <reference value="urn:uuid:dac358c3-403a-4dbb-b478-4259aed882ae"/>
        </result>
        <result>
          <reference value="urn:uuid:1d773d66-cec7-44a2-b92a-46d00adeae00"/>
        </result>
        <result>
          <reference value="urn:uuid:842d9ab9-d940-4f0c-adf9-e5c528f5c0e5"/>
        </result>
        <result>
          <reference value="urn:uuid:9a9f9a4a-52e3-4738-bd0b-a25374bbf358"/>
        </result>
        <result>
          <reference value="urn:uuid:58828523-8893-45fc-973b-16290366c5e5"/>
        </result>
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          <reference value="urn:uuid:2c28b23f-3e9f-4c03-8c8f-0e76bc5dc9c2"/>
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          <reference value="urn:uuid:1a71e80f-b044-4a91-80e1-eadbe5a53dca"/>
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      </DiagnosticReport>
    </resource>
    <request>
      <method value="POST"/>
      <url value="DiagnosticReport"/>
    </request>
  </entry>
</Bundle>