Genomics Reporting Implementation Guide
3.0.0 - STU3
Genomics Reporting Implementation Guide
3.0.0 - STU3
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-oncology-diagnostic-1"> </a><p class="res-header-id"><b>Generated Narrative: Patient Inline-Instance-for-oncology-diagnostic-1</b></p><a name="Inline-Instance-for-oncology-diagnostic-1"> </a><a name="hcInline-Instance-for-oncology-diagnostic-1"> </a><a name="Inline-Instance-for-oncology-diagnostic-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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<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Practitioner_Inline-Instance-for-oncology-diagnostic-2"> </a><p class="res-header-id"><b>Generated Narrative: Practitioner Inline-Instance-for-oncology-diagnostic-2</b></p><a name="Inline-Instance-for-oncology-diagnostic-2"> </a><a name="hcInline-Instance-for-oncology-diagnostic-2"> </a><a name="Inline-Instance-for-oncology-diagnostic-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>
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<name>
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<given value="Philip"/>
<given value="Prof"/>
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<state value="CA"/>
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<url value="Practitioner"/>
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<entry>
<fullUrl value="urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d"/>
<resource>
<Specimen>
<id value="Inline-Instance-for-oncology-diagnostic-3"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Specimen_Inline-Instance-for-oncology-diagnostic-3"> </a><p class="res-header-id"><b>Generated Narrative: Specimen Inline-Instance-for-oncology-diagnostic-3</b></p><a name="Inline-Instance-for-oncology-diagnostic-3"> </a><a name="hcInline-Instance-for-oncology-diagnostic-3"> </a><a name="Inline-Instance-for-oncology-diagnostic-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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<identifier>
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<status value="available"/>
<subject>
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<collection>
<collector>
<reference value="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"/>
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<url value="Specimen"/>
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<entry>
<fullUrl value="urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f"/>
<resource>
<Observation>
<id value="Inline-Instance-for-oncology-diagnostic-4"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker"/>
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<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncology-diagnostic-4"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-diagnostic-4</b></p><a name="Inline-Instance-for-oncology-diagnostic-4"> </a><a name="hcInline-Instance-for-oncology-diagnostic-4"> </a><a name="Inline-Instance-for-oncology-diagnostic-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>: 2019-03-05</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 Mutations/Megabase<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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<category>
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<coding>
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<code value="biomarker-category"/>
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<coding>
<system
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<code value="molgen"/>
<display value="molecular sequence adjacent category"/>
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<resource>
<Observation>
<id value="Inline-Instance-for-oncology-diagnostic-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-diagnostic-5"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-diagnostic-5</b></p><a name="Inline-Instance-for-oncology-diagnostic-5"> </a><a name="hcInline-Instance-for-oncology-diagnostic-5"> </a><a name="Inline-Instance-for-oncology-diagnostic-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-diagnostic.html#urn-uuid-d0b4affa-91d6-46d1-af01-b30d9f16ef6d">Bundle: type = transaction</a></p><p><b>effective</b>: 2019-03-05</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 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 81290-9}">Genomic DNA change (gHGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NC_000007.13:g.140453136A>T}">NC_000007.13:g.140453136A>T</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81252-9}">Discrete genetic variant</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/clinvar 13961}">Clinvar ID 13961</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_004324.2:p.Val600Glu}">NP_004324.2:p.Val600Glu</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:1097}">BRAF</span></p></blockquote></div>
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<status value="final"/>
<category>
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<code value="laboratory"/>
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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="69548-6"/>
<display value="Genetic variant assessment"/>
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<subject>
<reference value="urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"/>
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<effectiveDateTime value="2019-03-05"/>
<performer>
<reference value="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"/>
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<valueCodeableConcept>
<coding>
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<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"/>
</coding>
</method>
<specimen>
<reference value="urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d"/>
</specimen>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="62374-4"/>
<display value="Human reference sequence assembly version"/>
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</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA14029-5"/>
<display value="GRCh37"/>
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<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_000007.13:g.140453136A>T"/>
<display value="NC_000007.13:g.140453136A>T"/>
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</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81252-9"/>
<display value="Discrete genetic variant"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/clinvar"/>
<code value="13961"/>
<display value="Clinvar ID 13961"/>
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</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_004324.2:p.Val600Glu"/>
<display value="NP_004324.2:p.Val600Glu"/>
</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:1097"/>
<display value="BRAF"/>
</coding>
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</Observation>
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<request>
<method value="POST"/>
<url value="Observation"/>
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</entry>
<entry>
<fullUrl value="urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524"/>
<resource>
<Observation>
<id value="Inline-Instance-for-oncology-diagnostic-6"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"/>
</meta>
<text>
<status value="extensions"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_Inline-Instance-for-oncology-diagnostic-6"> </a><p class="res-header-id"><b>Generated Narrative: Observation Inline-Instance-for-oncology-diagnostic-6</b></p><a name="Inline-Instance-for-oncology-diagnostic-6"> </a><a name="hcInline-Instance-for-oncology-diagnostic-6"> </a><a name="Inline-Instance-for-oncology-diagnostic-6-en-US"> </a><p><b>Related artifact</b>: No display for RelatedArtifact (type: justification; display: https://pmkb.weill.cornell.edu/therapies/103)</p><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 diagnostic-implication}">Diagnostic 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>: 2019-03-05</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://loinc.org 53037-8}">Genetic variation clinical significance [Imp]</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6668-3}">Pathogenic</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:">melanoma</span></p></blockquote></div>
</text>
<extension
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<valueRelatedArtifact>
<type value="justification"/>
<display value="https://pmkb.weill.cornell.edu/therapies/103"/>
</valueRelatedArtifact>
</extension>
<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
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<code value="diagnostic-implication"/>
<display value="Diagnostic Implication"/>
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</code>
<subject>
<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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<method>
<coding>
<system value="http://loinc.org"/>
<code value="LA26811-2"/>
<display value="Computational analysis"/>
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<specimen>
<reference value="urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d"/>
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<derivedFrom>
<reference value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d"/>
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<code>
<coding>
<system value="http://loinc.org"/>
<code value="53037-8"/>
<display value="Genetic variation clinical significance [Imp]"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6668-3"/>
<display value="Pathogenic"/>
</coding>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="93044-6"/>
<display value="Level of Evidence"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA30200-2"/>
<display value="Very strong evidence pathogenic"/>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81259-4"/>
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<valueCodeableConcept>
<text value="melanoma"/>
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<method value="POST"/>
<url value="Observation"/>
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</entry>
<entry>
<fullUrl value="urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5"/>
<resource>
<DiagnosticReport>
<id value="Inline-Instance-for-oncology-diagnostic-7"/>
<meta>
<profile
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</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="DiagnosticReport_Inline-Instance-for-oncology-diagnostic-7"> </a><p class="res-header-id"><b>Generated Narrative: DiagnosticReport Inline-Instance-for-oncology-diagnostic-7</b></p><a name="Inline-Instance-for-oncology-diagnostic-7"> </a><a name="hcInline-Instance-for-oncology-diagnostic-7"> </a><a name="Inline-Instance-for-oncology-diagnostic-7-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>When For</td><td>2019-03-05</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></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>
<effectiveDateTime value="2019-03-05"/>
<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-99e4-48d603f3e12d"/>
<display value="BRAF V600E mutation observed"/>
</result>
<result>
<reference value="urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524"/>
<display value="melanoma implicated"/>
</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 2024-12-12
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