Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

: bundle-oncologyexamples-r4-withGrouping - XML Representation

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      <Patient>
        <id value="Inline-Instance-for-oncologyexamples-r4-withGrouping-1"/>
        <text>
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          <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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          <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>
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          <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>
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          <system value="http://unitsofmeasure.org"/>
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        <specimen>
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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-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>
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        <meta>
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          <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>
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          <valueCodeableConcept>
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        <hasMember>
          <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"/>
        </hasMember>
      </Observation>
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    <request>
      <method value="POST"/>
      <url value="Observation"/>
    </request>
  </entry>
  <entry>
    <fullUrl value="urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5"/>
    <resource>
      <DiagnosticReport>
        <id value="Inline-Instance-for-oncologyexamples-r4-withGrouping-15"/>
        <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-oncologyexamples-r4-withGrouping-15"> </a><p class="res-header-id"><b>Generated Narrative: DiagnosticReport Inline-Instance-for-oncologyexamples-r4-withGrouping-15</b></p><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-15"> </a><a name="hcInline-Instance-for-oncologyexamples-r4-withGrouping-15"> </a><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-15-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>Performer</td><td> <a href="Bundle-bundle-oncology-diagnostic.html#urn-uuid-a48256f8-db37-44e0-a0f6-d7af16c7c9ef">Bundle: type = transaction</a></td></tr></table><p><b>Report Details</b></p><table class="grid"><tr><td><b>Code</b></td><td><b>Value</b></td></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr></table></div>
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        <category>
          <coding>
            <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
            <code value="GE"/>
          </coding>
        </category>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="51969-4"/>
          </coding>
          <text value="Genetic analysis report"/>
        </code>
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          <reference value="urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"/>
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        <performer>
          <reference value="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"/>
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          <display value="Variants and other biomarker tests"/>
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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>
          <reference value="urn:uuid:772de7d7-e1bd-4183-bdb5-cea8eda317cd"/>
          <display value="SNV analysis for KDR variant"/>
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        <result>
          <reference value="urn:uuid:b33eb7ec-d83e-49d2-b0f3-729d024ebe01"/>
          <display value="SNV analysis for ERBB4 variant"/>
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        <result>
          <reference value="urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f"/>
          <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>
          <reference value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e"/>
          <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"/>
          <display value="Therapy match result 2"/>
        </result>
        <result>
          <reference value="urn:uuid:05713d1c-0df5-46d5-a5a9-2085eef56c20"/>
          <display value="Therapy match result 3"/>
        </result>
        <result>
          <reference value="urn:uuid:294f1401-e2eb-4df1-b6d2-09e1b7a6eca4"/>
          <display value="Therapy match result 4"/>
        </result>
      </DiagnosticReport>
    </resource>
    <request>
      <method value="POST"/>
      <url value="DiagnosticReport"/>
    </request>
  </entry>
</Bundle>