Genomics Reporting Implementation Guide
3.0.0 - STU3 International flag

This page is part of the Genetic Reporting Implementation Guide (v3.0.0: STU3) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version. For a full list of available versions, see the Directory of published versions

: bundle-oncologyexamples-r4-withGrouping - XML Representation

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<Bundle xmlns="http://hl7.org/fhir">
  <id value="bundle-oncologyexamples-r4-withGrouping"/>
  <type value="transaction"/>
  <entry>
    <fullUrl value="urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"/>
    <resource>
      <Patient>
        <id value="Inline-Instance-for-oncologyexamples-r4-withGrouping-1"/>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Patient_Inline-Instance-for-oncologyexamples-r4-withGrouping-1"> </a><p class="res-header-id"><b>Generated Narrative: Patient Inline-Instance-for-oncologyexamples-r4-withGrouping-1</b></p><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-1"> </a><a name="hcInline-Instance-for-oncologyexamples-r4-withGrouping-1"> </a><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-1-en-US"> </a><p style="border: 1px #661aff solid; background-color: #e6e6ff; padding: 10px;">Carrot John Mr  Male, DoB: 1962-12-31 ( 1007)</p><hr/><table class="grid"><tr><td style="background-color: #f3f5da" title="Patient Links">Links:</td><td colspan="3"><ul><li>General Practitioner: <a href="Bundle-bundle-oncology-diagnostic.html#urn-uuid-a48256f8-db37-44e0-a0f6-d7af16c7c9ef">Bundle: type = transaction</a></li></ul></td></tr></table></div>
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          <given value="Carrot"/>
          <given value="John"/>
          <given value="Mr"/>
        </name>
        <gender value="male"/>
        <birthDate value="1962-12-31"/>
        <generalPractitioner>
          <reference value="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"/>
        </generalPractitioner>
      </Patient>
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      <method value="POST"/>
      <url value="Patient"/>
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  <entry>
    <fullUrl value="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"/>
    <resource>
      <Practitioner>
        <id value="Inline-Instance-for-oncologyexamples-r4-withGrouping-2"/>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Practitioner_Inline-Instance-for-oncologyexamples-r4-withGrouping-2"> </a><p class="res-header-id"><b>Generated Narrative: Practitioner Inline-Instance-for-oncologyexamples-r4-withGrouping-2</b></p><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-2"> </a><a name="hcInline-Instance-for-oncologyexamples-r4-withGrouping-2"> </a><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-2-en-US"> </a><p><b>identifier</b>: 4654765876</p><p><b>name</b>: Akerman Philip Prof </p><p><b>address</b>: Castro Valley CA </p></div>
        </text>
        <identifier>
          <value value="4654765876"/>
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        <name>
          <given value="Akerman"/>
          <given value="Philip"/>
          <given value="Prof"/>
        </name>
        <address>
          <city value="Castro Valley"/>
          <state value="CA"/>
        </address>
      </Practitioner>
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    <request>
      <method value="POST"/>
      <url value="Practitioner"/>
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  <entry>
    <fullUrl value="urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d"/>
    <resource>
      <Specimen>
        <id value="Inline-Instance-for-oncologyexamples-r4-withGrouping-3"/>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Specimen_Inline-Instance-for-oncologyexamples-r4-withGrouping-3"> </a><p class="res-header-id"><b>Generated Narrative: Specimen Inline-Instance-for-oncologyexamples-r4-withGrouping-3</b></p><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-3"> </a><a name="hcInline-Instance-for-oncologyexamples-r4-withGrouping-3"> </a><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-3-en-US"> </a><p><b>identifier</b>: 076e1948-2217-11e9-94d8-12e241dc1f66</p><p><b>status</b>: Available</p><p><b>subject</b>: <a href="Bundle-bundle-oncology-diagnostic.html#urn-uuid-d0b4affa-91d6-46d1-af01-b30d9f16ef6d">Bundle: type = transaction</a></p><h3>Collections</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Collector</b></td></tr><tr><td style="display: none">*</td><td><a href="Bundle-bundle-oncology-diagnostic.html#urn-uuid-a48256f8-db37-44e0-a0f6-d7af16c7c9ef">Bundle: type = transaction</a></td></tr></table></div>
        </text>
        <identifier>
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        </identifier>
        <status value="available"/>
        <subject>
          <reference value="urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"/>
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        <collection>
          <collector>
            <reference value="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"/>
          </collector>
        </collection>
      </Specimen>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Specimen"/>
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  </entry>
  <entry>
    <fullUrl value="urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f"/>
    <resource>
      <Observation>
        <id value="Inline-Instance-for-oncologyexamples-r4-withGrouping-4"/>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncologyexamples-r4-withGrouping-4"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncologyexamples-r4-withGrouping-4</b></p><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-4"> </a><a name="hcInline-Instance-for-oncologyexamples-r4-withGrouping-4"> </a><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs biomarker-category}">A characterization of a given biomarker observation.</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 94076-7}">Mutations/Megabase [# Ratio] in Tumor</span></p><p><b>subject</b>: <a href="Bundle-bundle-oncology-diagnostic.html#urn-uuid-d0b4affa-91d6-46d1-af01-b30d9f16ef6d">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-05-01</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-diagnostic.html#urn-uuid-a48256f8-db37-44e0-a0f6-d7af16c7c9ef">Bundle: type = transaction</a></p><p><b>value</b>: 25 somatic variants per megabase of sequenced DNA<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1/1000000 = '1/1000000')</span></p><p><b>specimen</b>: <a href="Bundle-bundle-oncology-diagnostic.html#urn-uuid-a5d6a6a9-4859-480e-85b2-56974fef3b9d">Bundle: type = transaction</a></p><h3>Components</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs biomarker-category}">A characterization of a given biomarker observation.</span></td><td><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/molecular-biomarker-ontology-cs molgen}">molecular sequence adjacent category</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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
            <code value="biomarker-category"/>
          </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="94076-7"/>
            <display value="Mutations/Megabase [# Ratio] in Tumor"/>
          </coding>
        </code>
        <subject>
          <reference value="urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"/>
        </subject>
        <effectiveDateTime value="2023-05-01"/>
        <performer>
          <reference value="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"/>
        </performer>
        <valueQuantity>
          <value value="25"/>
          <unit value="somatic variants per megabase of sequenced DNA"/>
          <system value="http://unitsofmeasure.org"/>
          <code value="1/1000000"/>
        </valueQuantity>
        <specimen>
          <reference value="urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d"/>
        </specimen>
        <component>
          <code>
            <coding>
              <system
                      value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
              <code value="biomarker-category"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system
                      value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/molecular-biomarker-ontology-cs"/>
              <code value="molgen"/>
              <display value="molecular sequence adjacent category"/>
            </coding>
          </valueCodeableConcept>
        </component>
      </Observation>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="urn:uuid:64b91716-6431-41bd-8fd4-7ac99bebdee9"/>
    <resource>
      <Observation>
        <id value="Inline-Instance-for-oncologyexamples-r4-withGrouping-5"/>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncologyexamples-r4-withGrouping-5"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncologyexamples-r4-withGrouping-5</b></p><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-5"> </a><a name="hcInline-Instance-for-oncologyexamples-r4-withGrouping-5"> </a><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs biomarker-category}">A characterization of a given biomarker observation.</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 81695-9}">Microsatellite instability [Interpretation] in Cancer specimen Qualitative</span></p><p><b>subject</b>: <a href="Bundle-bundle-oncology-diagnostic.html#urn-uuid-d0b4affa-91d6-46d1-af01-b30d9f16ef6d">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-05-01</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-diagnostic.html#urn-uuid-a48256f8-db37-44e0-a0f6-d7af16c7c9ef">Bundle: type = transaction</a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA14122-8}">Stable</span></p><p><b>specimen</b>: <a href="Bundle-bundle-oncology-diagnostic.html#urn-uuid-a5d6a6a9-4859-480e-85b2-56974fef3b9d">Bundle: type = transaction</a></p><h3>Components</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs biomarker-category}">A characterization of a given biomarker observation.</span></td><td><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/molecular-biomarker-ontology-cs molgen}">molecular sequence adjacent category</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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
            <code value="biomarker-category"/>
          </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="81695-9"/>
            <display
                     value="Microsatellite instability [Interpretation] in Cancer specimen Qualitative"/>
          </coding>
        </code>
        <subject>
          <reference value="urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"/>
        </subject>
        <effectiveDateTime value="2023-05-01"/>
        <performer>
          <reference value="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"/>
        </performer>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA14122-8"/>
            <display value="Stable"/>
          </coding>
        </valueCodeableConcept>
        <specimen>
          <reference value="urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d"/>
        </specimen>
        <component>
          <code>
            <coding>
              <system
                      value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
              <code value="biomarker-category"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system
                      value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/molecular-biomarker-ontology-cs"/>
              <code value="molgen"/>
              <display value="molecular sequence adjacent category"/>
            </coding>
          </valueCodeableConcept>
        </component>
      </Observation>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d"/>
    <resource>
      <Observation>
        <id value="Inline-Instance-for-oncologyexamples-r4-withGrouping-6"/>
        <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-oncologyexamples-r4-withGrouping-6"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncologyexamples-r4-withGrouping-6</b></p><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-6"> </a><a name="hcInline-Instance-for-oncologyexamples-r4-withGrouping-6"> </a><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-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-diagnostic.html#urn-uuid-d0b4affa-91d6-46d1-af01-b30d9f16ef6d">Bundle: type = transaction</a></p><p><b>effective</b>: 2023-05-01</p><p><b>performer</b>: <a href="Bundle-bundle-oncology-diagnostic.html#urn-uuid-a48256f8-db37-44e0-a0f6-d7af16c7c9ef">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>: <a href="Bundle-bundle-oncology-diagnostic.html#urn-uuid-a5d6a6a9-4859-480e-85b2-56974fef3b9d">Bundle: type = transaction</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81290-9}">Genomic DNA change (gHGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NC_000009.12:g.5073770G&gt;T}">NC_000009.12:g.5073770G&gt;T</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_004963.1:p.Val617Phe}">NP_004963.1:p.Val617Phe</span></p></blockquote><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 LA6683-2}">Germline</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:">JAK2</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:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"/>
        </subject>
        <effectiveDateTime value="2023-05-01"/>
        <performer>
          <reference value="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"/>
        </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>
          <reference value="urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d"/>
        </specimen>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="81290-9"/>
              <display value="Genomic DNA change (gHGVS)"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://varnomen.hgvs.org"/>
              <code value="NC_000009.12:g.5073770G&gt;T"/>
              <display value="NC_000009.12:g.5073770G&gt;T"/>
            </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_004963.1:p.Val617Phe"/>
              <display value="NP_004963.1:p.Val617Phe"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <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="LA6683-2"/>
              <display value="Germline"/>
            </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"/>
              <display value="JAK2"/>
            </coding>
          </valueCodeableConcept>
        </component>
      </Observation>
    </resource>
    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="urn:uuid:772de7d7-e1bd-4183-bdb5-cea8eda317cd"/>
    <resource>
      <Observation>
        <id value="Inline-Instance-for-oncologyexamples-r4-withGrouping-7"/>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
        </meta>
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          <display value="Therapy match result 1"/>
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        <hasMember>
          <reference value="urn:uuid:1301943b-55db-4adf-8355-3635f7268a1b"/>
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          <reference value="urn:uuid:05713d1c-0df5-46d5-a5a9-2085eef56c20"/>
          <display value="Therapy match result 3"/>
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        <hasMember>
          <reference value="urn:uuid:294f1401-e2eb-4df1-b6d2-09e1b7a6eca4"/>
          <display value="Therapy match result 4"/>
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        <meta>
          <profile
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        <text>
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          <coding>
            <system value="http://loinc.org"/>
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          <text value="Genetic analysis report"/>
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        <result>
          <reference value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d"/>
          <display value="SNV analysis for JAK2 variant"/>
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        <result>
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          <display value="SNV analysis for KDR variant"/>
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          <display value="SNV analysis for ERBB4 variant"/>
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        <result>
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          <display value="TMB value analysis"/>
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        <result>
          <reference value="urn:uuid:64b91716-6431-41bd-8fd4-7ac99bebdee9"/>
          <display value="MSI status analysis"/>
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        <result>
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          <display value="Therapy Match Results"/>
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        <result>
          <reference value="urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524"/>
          <display value="Therapy match result 1"/>
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        <result>
          <reference value="urn:uuid:1301943b-55db-4adf-8355-3635f7268a1b"/>
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        <result>
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          <display value="Therapy match result 3"/>
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        <result>
          <reference value="urn:uuid:294f1401-e2eb-4df1-b6d2-09e1b7a6eca4"/>
          <display value="Therapy match result 4"/>
        </result>
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    </resource>
    <request>
      <method value="POST"/>
      <url value="DiagnosticReport"/>
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</Bundle>