Genomics Reporting Implementation Guide (STU1)
This page is part of the Genetic Reporting Implementation Guide (v1.0.0: STU 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions 
<Bundle xmlns="http://hl7.org/fhir"> <id value="oncology-diagnostic"/> <type value="transaction"/> <entry> <fullUrl value="urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"/> <resource> <Patient> <text> <status value="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative with Details</b></p><p><b>identifier</b>: 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="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef">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> <text> <status value="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative with Details</b></p><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"/> </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> <meta> <profile value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/specimen"/> </meta> <text> <status value="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative with Details</b></p><p><b>meta</b>: </p><p><b>identifier</b>: 076e1948-2217-11e9-94d8-12e241dc1f66</p><p><b>status</b>: available</p><p><b>subject</b>: <a href="urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d">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="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef">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> <text> <status value="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative with Details</b></p><p><b>status</b>: final</p><p><b>code</b>: Tumor Mutational Burden <span style="background: LightGoldenRodYellow">(Details )</span></p><p><b>subject</b>: <a href="urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d">urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d</a></p><p><b>performer</b>: <a href="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef">urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef</a></p><p><b>value</b>: 25.0 somatic variants per megabase of sequenced DNA<span style="background: LightGoldenRodYellow"> (Details: UCUM code v/Mb = 'v/Mb')</span></p><p><b>specimen</b>: <a href="urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d">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="25.0"/> <unit value="somatic variants per megabase of sequenced DNA"/> <system value="http://unitsofmeasure.org"/> <code value="v/Mb"/> </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> <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 with Details</b></p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style="background: LightGoldenRodYellow">(Details : {LOINC code '69548-6' = 'Genetic variant assessment', given as 'Genetic variant assessment'})</span></p><p><b>subject</b>: <a href="urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d">urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d</a></p><p><b>performer</b>: <a href="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef">urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef</a></p><p><b>value</b>: Present <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA9633-4' = 'Present', given as 'Present'})</span></p><p><b>method</b>: Sequencing <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA26398-0' = 'Sequencing', given as 'Sequencing'})</span></p><p><b>specimen</b>: <a href="urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d">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">(Details : {LOINC code '62374-4' = 'Human reference sequence assembly version', given as 'Human reference sequence assembly version'})</span></p><p><b>value</b>: GRCh37 <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA14029-5' = 'GRCh37', given as 'GRCh37'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic DNA change (gHGVS) <span style="background: LightGoldenRodYellow">(Details : {LOINC code '81290-9' = 'Genomic DNA change (gHGVS)', given as 'Genomic DNA change (gHGVS)'})</span></p><p><b>value</b>: NC_000007.13:g.140453136A>T <span style="background: LightGoldenRodYellow">(Details : {http://varnomen.hgvs.org code 'NC_000007.13:g.140453136A>T' = 'NC_000007.13:g.140453136A>T', given as '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">(Details : {LOINC code '81252-9' = 'Discrete genetic variant', given as 'Discrete genetic variant'})</span></p><p><b>value</b>: Clinvar ID 13961 <span style="background: LightGoldenRodYellow">(Details : {http://www.ncbi.nlm.nih.gov/clinvar code '13961' = '13961', given as 'Clinvar ID 13961'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change (pHGVS) <span style="background: LightGoldenRodYellow">(Details : {LOINC code '48005-3' = 'Amino acid change (pHGVS)', given as 'Amino acid change (pHGVS)'})</span></p><p><b>value</b>: p.Val600Glu <span style="background: LightGoldenRodYellow">(Details : {http://varnomen.hgvs.org code 'p.Val600Glu' = 'p.Val600Glu', given as 'p.Val600Glu'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change type <span style="background: LightGoldenRodYellow">(Details : {LOINC code '48006-1' = 'Amino acid change [Type]', given as 'Amino acid change type'})</span></p><p><b>value</b>: Missense <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA6698-0' = 'Missense', given as 'Missense'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied ID <span style="background: LightGoldenRodYellow">(Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'})</span></p><p><b>value</b>: BRAF <span style="background: LightGoldenRodYellow">(Details : {http://www.genenames.org/geneId code 'HGNC:1097' = 'HGNC:1097', given as 'BRAF'})</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> <meta> <profile value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/somatic-diagnostic"/> </meta> <text> <status value="generated"/> <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative with Details</b></p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: somatic-diagnostic <span style="background: LightGoldenRodYellow">(Details : {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes code 'somatic-diagnostic' = 'somatic-diagnostic)</span></p><p><b>subject</b>: <a href="urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d">urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d</a></p><p><b>performer</b>: <a href="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef">urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef</a></p><p><b>value</b>: Supportive <span style="background: LightGoldenRodYellow">(Details )</span></p><p><b>method</b>: Computational analysis <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA26811-2' = 'Computational analysis', given as 'Computational analysis'})</span></p><p><b>specimen</b>: <a href="urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d">urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d</a></p><p><b>derivedFrom</b>: <a href="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d">urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Level of Evidence <span style="background: LightGoldenRodYellow">(Details : {LOINC code '93044-6' = 'Level of evidence', given as 'Level of Evidence'})</span></p><p><b>value</b>: AMP/ASCO/CAP guidelines - Level A <span style="background: LightGoldenRodYellow">(Details )</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: associated-cancer <span style="background: LightGoldenRodYellow">(Details : {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes code 'associated-cancer' = 'associated-cancer)</span></p><p><b>value</b>: melanoma <span style="background: LightGoldenRodYellow">(Details )</span></p></blockquote></div> </text> <extension url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/RelatedArtifact"> <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"/> <code value="somatic-diagnostic"/> </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> <text value="Supportive"/> </valueCodeableConcept> <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="93044-6"/> <display value="Level of Evidence"/> </coding> </code> <valueCodeableConcept> <!-- coding> <system value="AMP/ASCO/CAP guidelines"/> <code value="A"/> <display value="Level A evidence"/> </coding --> <text value="AMP/ASCO/CAP guidelines - Level A"/> </valueCodeableConcept> </component> <component> <code> <coding> <system value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes"/> <code value="associated-cancer"/> </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> <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 with Details</b></p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>code</b>: Genetic analysis report <span style="background: LightGoldenRodYellow">(Details : {LOINC code '81247-9' = 'Master HL7 genetic variant reporting panel', given as 'Master HL7 genetic variant reporting panel'})</span></p><p><b>subject</b>: <a href="urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d">urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d</a></p><p><b>performer</b>: <a href="urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef">urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef</a></p><p><b>specimen</b>: <a href="urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d">urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d</a></p><p><b>result</b>: </p><ul><li><a href="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d">BRAF V600E mutation observed</a></li><li><a href="urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524">melanoma implicated</a></li></ul></div> </text> <status value="final"/> <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 © 2017+ HL7 International Clinical Genomics Work Group. Package hl7.fhir.uv.genomics-reporting#1.0.0 based on FHIR 4.0.1. Generated 2019-11-20
Links: Table of Contents |
QA Report | Search |
Version History |
|
Propose a change