Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide
3.0.0 - release
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
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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="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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<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>T}">NC_000009.12:g.5073770G>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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<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncologyexamples-r4-withGrouping-9"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncologyexamples-r4-withGrouping-9</b></p><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-9"> </a><a name="hcInline-Instance-for-oncologyexamples-r4-withGrouping-9"> </a><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}">Therapeutic Implication</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>method</b>: <span title="Codes:{http://loinc.org LA26811-2}">Computational analysis</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><p><b>derivedFrom</b>: <a href="Bundle-bundle-complexVariant-nonHGVS.html#urn-uuid-16fdd5fc-e665-48af-99e4-48d603f3e12d">Bundle: type = transaction</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}">Therapeutic Implication</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6677-4}">Responsive</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 93044-6}">Level of evidence</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA30200-2}">Very strong evidence pathogenic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81259-4}">Associated phenotype</span></p><p><b>value</b>: <span title="Codes:">Polycythemia vera (PV)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>Medication Assessed reference to a FHIR resource</b>: <a href="#hcInline-Instance-for-oncologyexamples-r4-withGrouping-9/Inline-MedicationKnowledgeRuxolitinib">MedicationKnowledge Ruxolitinib</a></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51963-7}">Medication assessed [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.nlm.nih.gov/research/umls/rxnorm 1193326}">Ruxolitinib</span></p></blockquote><hr/><blockquote><p class="res-header-id"><b>Generated Narrative: MedicationKnowledge #Inline-MedicationKnowledgeRuxolitinib</b></p><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-9/Inline-MedicationKnowledgeRuxolitinib"> </a><a name="hcInline-Instance-for-oncologyexamples-r4-withGrouping-9/Inline-MedicationKnowledgeRuxolitinib"> </a><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-9/Inline-MedicationKnowledgeRuxolitinib-en-US"> </a><p><b>code</b>: <span title="Codes:{http://www.nlm.nih.gov/research/umls/rxnorm 1193326}">Ruxolitinib</span></p><p><b>status</b>: Active</p></blockquote></div>
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<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncologyexamples-r4-withGrouping-12"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncologyexamples-r4-withGrouping-12</b></p><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-12"> </a><a name="hcInline-Instance-for-oncologyexamples-r4-withGrouping-12"> </a><a name="Inline-Instance-for-oncologyexamples-r4-withGrouping-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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}">Therapeutic Implication</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>method</b>: <span title="Codes:{http://loinc.org LA26811-2}">Computational analysis</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><p><b>derivedFrom</b>: <a href="Bundle-bundle-complexVariant-nonHGVS.html#urn-uuid-16fdd5fc-e665-48af-99e4-48d603f3e12d">Bundle: type = transaction</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}">Therapeutic Implication</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6677-4}">Responsive</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 93044-6}">Level of Evidence</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA30200-2}">Very strong evidence pathogenic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81259-4}">Associated phenotype</span></p><p><b>value</b>: <span title="Codes:">Polycythemia vera (PV)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 51963-7}">Medication assessed</span></p><p><b>value</b>: <span title="Codes:">TG02</span></p></blockquote></div>
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<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>
</text>
<status value="final"/>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51969-4"/>
</coding>
<text value="Genetic analysis report"/>
</code>
<subject>
<reference value="urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"/>
</subject>
<performer>
<reference value="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"/>
</performer>
<specimen>
<reference value="urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d"/>
</specimen>
<result>
<reference value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12f"/>
<display value="Variants and other biomarker tests"/>
</result>
<result>
<reference value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d"/>
<display value="SNV analysis for JAK2 variant"/>
</result>
<result>
<reference value="urn:uuid:772de7d7-e1bd-4183-bdb5-cea8eda317cd"/>
<display value="SNV analysis for KDR variant"/>
</result>
<result>
<reference value="urn:uuid:b33eb7ec-d83e-49d2-b0f3-729d024ebe01"/>
<display value="SNV analysis for ERBB4 variant"/>
</result>
<result>
<reference value="urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f"/>
<display value="TMB value analysis"/>
</result>
<result>
<reference value="urn:uuid:64b91716-6431-41bd-8fd4-7ac99bebdee9"/>
<display value="MSI status analysis"/>
</result>
<result>
<reference value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e"/>
<display value="Therapy Match Results"/>
</result>
<result>
<reference value="urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524"/>
<display value="Therapy match result 1"/>
</result>
<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>
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-11-19
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