Genomics Reporting Implementation Guide
2.0.0 - trial-use
Genomics Reporting Implementation Guide
2.0.0 - trial-use
This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version. For a full list of available versions, see the Directory of published versions 
<Bundle xmlns="http://hl7.org/fhir">
<id value="bundle-oncology-diagnostic"/>
<type value="transaction"/>
<entry>
<fullUrl value="urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"/>
<resource>
<Patient>
<id value="Inline-Instance-for-oncology-diagnostic-1"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "Inline-Instance-for-oncology-diagnostic-1" </p></div><p><b>identifier</b>: id: 1007</p><p><b>name</b>: Carrot John Mr </p><p><b>gender</b>: male</p><p><b>birthDate</b>: 1962-12-31</p><p><b>generalPractitioner</b>: <a href="#Practitioner_Inline-Instance-for-oncology-diagnostic-2">See above (urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef)</a></p></div>
</text>
<identifier>
<value value="1007"/>
</identifier>
<name>
<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>
</resource>
<request>
<method value="POST"/>
<url value="Patient"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"/>
<resource>
<Practitioner>
<id value="Inline-Instance-for-oncology-diagnostic-2"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "Inline-Instance-for-oncology-diagnostic-2" </p></div><p><b>identifier</b>: id: 4654765876</p><p><b>name</b>: Akerman Philip Prof </p><p><b>address</b>: Castro Valley CA </p></div>
</text>
<identifier>
<value value="4654765876"/>
</identifier>
<name>
<given value="Akerman"/>
<given value="Philip"/>
<given value="Prof"/>
</name>
<address>
<city value="Castro Valley"/>
<state value="CA"/>
</address>
</Practitioner>
</resource>
<request>
<method value="POST"/>
<url value="Practitioner"/>
</request>
</entry>
<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"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "Inline-Instance-for-oncology-diagnostic-3" </p></div><p><b>identifier</b>: id: 076e1948-2217-11e9-94d8-12e241dc1f66</p><p><b>status</b>: available</p><p><b>subject</b>: <a href="#Patient_Inline-Instance-for-oncology-diagnostic-1">See above (urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d)</a></p><h3>Collections</h3><table class="grid"><tr><td>-</td><td><b>Collector</b></td></tr><tr><td>*</td><td><a href="#Practitioner_Inline-Instance-for-oncology-diagnostic-2">See above (urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef)</a></td></tr></table></div>
</text>
<identifier>
<value value="076e1948-2217-11e9-94d8-12e241dc1f66"/>
</identifier>
<status value="available"/>
<subject>
<reference value="urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"/>
</subject>
<collection>
<collector>
<reference value="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"/>
</collector>
</collection>
</Specimen>
</resource>
<request>
<method value="POST"/>
<url value="Specimen"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f"/>
<resource>
<Observation>
<id value="Inline-Instance-for-oncology-diagnostic-4"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "Inline-Instance-for-oncology-diagnostic-4" </p></div><p><b>status</b>: final</p><p><b>code</b>: Tumor Mutational Burden <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> ()</span></p><p><b>subject</b>: <a href="#Patient_Inline-Instance-for-oncology-diagnostic-1">See above (urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d)</a></p><p><b>performer</b>: <a href="#Practitioner_Inline-Instance-for-oncology-diagnostic-2">See above (urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef)</a></p><p><b>value</b>: 25 Mutations/Megabase<span style="background: LightGoldenRodYellow"> (Details: UCUM code 1/1000000{Base} = '1/1000000{Base}')</span></p><p><b>specimen</b>: <a href="#Specimen_Inline-Instance-for-oncology-diagnostic-3">See above (urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d)</a></p></div>
</text>
<status value="final"/>
<code>
<text value="Tumor Mutational Burden"/>
</code>
<subject>
<reference value="urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"/>
</subject>
<performer>
<reference value="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"/>
</performer>
<valueQuantity>
<value value="25"/>
<unit value="Mutations/Megabase"/>
<system value="http://unitsofmeasure.org"/>
<code value="1/1000000{Base}"/>
</valueQuantity>
<specimen>
<reference value="urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d"/>
</specimen>
</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-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"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "Inline-Instance-for-oncology-diagnostic-5" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-variant.html">Variant</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69548-6)</span></p><p><b>subject</b>: <a href="#Patient_Inline-Instance-for-oncology-diagnostic-1">See above (urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d)</a></p><p><b>performer</b>: <a href="#Practitioner_Inline-Instance-for-oncology-diagnostic-2">See above (urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef)</a></p><p><b>value</b>: Present <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA9633-4)</span></p><p><b>method</b>: Sequencing <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA26398-0)</span></p><p><b>specimen</b>: <a href="#Specimen_Inline-Instance-for-oncology-diagnostic-3">See above (urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Human reference sequence assembly version <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#62374-4)</span></p><p><b>value</b>: GRCh37 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA14029-5)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic DNA change (gHGVS) <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81290-9)</span></p><p><b>value</b>: NC_000007.13:g.140453136A>T <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-v3-hgvs.html">Human Genome Variation Society nomenclature</a>#NC_000007.13:g.140453136A>T)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Discrete genetic variant <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81252-9)</span></p><p><b>value</b>: Clinvar ID 13961 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (clinvar#13961)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change (pHGVS) <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48005-3)</span></p><p><b>value</b>: p.Val600Glu <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-v3-hgvs.html">Human Genome Variation Society nomenclature</a>#p.Val600Glu)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change type <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48006-1)</span></p><p><b>value</b>: Missense <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA6698-0)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied ID <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48018-6)</span></p><p><b>value</b>: BRAF <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (geneId#HGNC:1097)</span></p></blockquote></div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</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>
<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="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="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"/>
</coding>
</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"/>
</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="p.Val600Glu"/>
<display value="p.Val600Glu"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48006-1"/>
<display value="Amino acid change type"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6698-0"/>
<display value="Missense"/>
</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/geneId"/>
<code value="HGNC:1097"/>
<display value="BRAF"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
<request>
<method value="POST"/>
<url value="Observation"/>
</request>
</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"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "Inline-Instance-for-oncology-diagnostic-6" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-diagnostic-implication.html">Diagnostic Implication</a></p></div><p><b>Genomics Artifact</b>: </p><p><b style="color: maroon">Exception generating Narrative: type org.hl7.fhir.r5.model.RelatedArtifact not handled - should not be here</b></p></div>
</text>
<extension
url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-artifact">
<valueRelatedArtifact>
<type value="justification"/>
<display value="https://pmkb.weill.cornell.edu/therapies/103"/>
</valueRelatedArtifact>
</extension>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
<code value="diagnostic-implication"/>
<display value="Diagnostic Implication"/>
</coding>
</code>
<subject>
<reference value="urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"/>
</subject>
<performer>
<reference value="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"/>
</performer>
<method>
<coding>
<system value="http://loinc.org"/>
<code value="LA26811-2"/>
<display value="Computational analysis"/>
</coding>
</method>
<specimen>
<reference value="urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d"/>
</specimen>
<derivedFrom>
<reference value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d"/>
</derivedFrom>
<component>
<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>
</valueCodeableConcept>
</component>
<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"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81259-4"/>
</coding>
</code>
<valueCodeableConcept>
<text value="melanoma"/>
</valueCodeableConcept>
</component>
</Observation>
</resource>
<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-oncology-diagnostic-7"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "Inline-Instance-for-oncology-diagnostic-7" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-genomics-report.html">Genomics Report</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Genetics <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-v2-0074.html">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Genetic analysis report <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81247-9 "Master HL7 genetic variant reporting panel")</span></p><p><b>subject</b>: <a href="#Patient_Inline-Instance-for-oncology-diagnostic-1">See above (urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d)</a></p><p><b>performer</b>: <a href="#Practitioner_Inline-Instance-for-oncology-diagnostic-2">See above (urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef)</a></p><p><b>specimen</b>: <a href="#Specimen_Inline-Instance-for-oncology-diagnostic-3">See above (urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d)</a></p><p><b>result</b>: </p><ul><li><a href="#Observation_Inline-Instance-for-oncology-diagnostic-5">See above (urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d: BRAF V600E mutation observed)</a></li><li><a href="#Observation_Inline-Instance-for-oncology-diagnostic-6">See above (urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524: melanoma implicated)</a></li></ul></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="81247-9"/>
<display value="Master HL7 genetic variant reporting panel"/>
</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-99e4-48d603f3e12d"/>
<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 Clinical Genomics Working Group. Package hl7.fhir.uv.genomics-reporting#2.0.0 based on FHIR 4.0.1. Generated 2022-05-09
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