Genomics Reporting Implementation Guide
1.1.0 - Ballot
Genomics Reporting Implementation Guide
1.1.0 - Ballot
This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 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 
@prefix fhir: <http://hl7.org/fhir/> .
@prefix loinc: <http://loinc.org/rdf#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
# - resource -------------------------------------------------------------------
a fhir:Bundle;
fhir:nodeRole fhir:treeRoot;
fhir:Resource.id [ fhir:value "oncology-diagnostic"];
fhir:Bundle.type [ fhir:value "transaction"];
fhir:Bundle.entry [
fhir:index 0;
fhir:Bundle.entry.fullUrl [ fhir:value "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d" ];
fhir:Bundle.entry.resource <urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Patient" ] ]
], [
fhir:index 1;
fhir:Bundle.entry.fullUrl [ fhir:value "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef" ];
fhir:Bundle.entry.resource <urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Practitioner" ] ]
], [
fhir:index 2;
fhir:Bundle.entry.fullUrl [ fhir:value "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d" ];
fhir:Bundle.entry.resource <urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Specimen" ] ]
], [
fhir:index 3;
fhir:Bundle.entry.fullUrl [ fhir:value "urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f" ];
fhir:Bundle.entry.resource <urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ]
], [
fhir:index 4;
fhir:Bundle.entry.fullUrl [ fhir:value "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d" ];
fhir:Bundle.entry.resource <urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ]
], [
fhir:index 5;
fhir:Bundle.entry.fullUrl [ fhir:value "urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524" ];
fhir:Bundle.entry.resource <urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ]
], [
fhir:index 6;
fhir:Bundle.entry.fullUrl [ fhir:value "urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5" ];
fhir:Bundle.entry.resource <urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "DiagnosticReport" ] ]
].
<urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d> a fhir:Patient;
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><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=\"#urnuuida48256f8-db37-44e0-a0f6-d7af16c7c9ef\">See above (Practitioner/null)</a></p></div>"
];
fhir:Patient.identifier [
fhir:index 0;
fhir:Identifier.value [ fhir:value "1007" ]
];
fhir:Patient.name [
fhir:index 0;
fhir:HumanName.given [
fhir:value "Carrot";
fhir:index 0 ], [
fhir:value "John";
fhir:index 1 ], [
fhir:value "Mr";
fhir:index 2 ]
];
fhir:Patient.gender [ fhir:value "male"];
fhir:Patient.birthDate [ fhir:value "1962-12-31"^^xsd:date];
fhir:Patient.generalPractitioner [
fhir:index 0;
fhir:Reference.reference [ fhir:value "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef" ]
].
<urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef> a fhir:Practitioner;
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p><b>identifier</b>: id: 4654765876</p><p><b>name</b>: Akerman Philip Prof </p><p><b>address</b>: Castro Valley CA </p></div>"
];
fhir:Practitioner.identifier [
fhir:index 0;
fhir:Identifier.value [ fhir:value "4654765876" ]
];
fhir:Practitioner.name [
fhir:index 0;
fhir:HumanName.given [
fhir:value "Akerman";
fhir:index 0 ], [
fhir:value "Philip";
fhir:index 1 ], [
fhir:value "Prof";
fhir:index 2 ]
];
fhir:Practitioner.address [
fhir:index 0;
fhir:Address.city [ fhir:value "Castro Valley" ];
fhir:Address.state [ fhir:value "CA" ]
].
<urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d> a fhir:Specimen;
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/specimen";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/specimen> ]
];
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p><b>identifier</b>: id: 076e1948-2217-11e9-94d8-12e241dc1f66</p><p><b>status</b>: available</p><p><b>subject</b>: <a href=\"#urnuuidd0b4affa-91d6-46d1-af01-b30d9f16ef6d\">See above (Patient/null)</a></p><h3>Collections</h3><table class=\"grid\"><tr><td>-</td><td><b>Collector</b></td></tr><tr><td>*</td><td><a href=\"#urnuuida48256f8-db37-44e0-a0f6-d7af16c7c9ef\">See above (Practitioner/null)</a></td></tr></table></div>"
];
fhir:Specimen.identifier [
fhir:index 0;
fhir:Identifier.value [ fhir:value "076e1948-2217-11e9-94d8-12e241dc1f66" ]
];
fhir:Specimen.status [ fhir:value "available"];
fhir:Specimen.subject [
fhir:Reference.reference [ fhir:value "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d" ]
];
fhir:Specimen.collection [
fhir:Specimen.collection.collector [
fhir:Reference.reference [ fhir:value "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef" ] ]
].
<urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f> a fhir:Observation;
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p></p><p><b>code</b>: <span title=\"Codes: \">Tumor Mutational Burden</span></p><p><b>subject</b>: <a href=\"#urnuuidd0b4affa-91d6-46d1-af01-b30d9f16ef6d\">See above (Patient/null)</a></p><p><b>performer</b>: <a href=\"#urnuuida48256f8-db37-44e0-a0f6-d7af16c7c9ef\">See above (Practitioner/null)</a></p><p><b>value</b>: 25.0 Mutations/Megabase</p><p><b>specimen</b>: <a href=\"#urnuuida5d6a6a9-4859-480e-85b2-56974fef3b9d\">See above (Specimen/null)</a></p></div>"
];
fhir:Observation.status [ fhir:value "final"];
fhir:Observation.code [
fhir:CodeableConcept.text [ fhir:value "Tumor Mutational Burden" ]
];
fhir:Observation.subject [
fhir:Reference.reference [ fhir:value "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d" ]
];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef" ]
];
fhir:Observation.valueQuantity [
fhir:Quantity.value [ fhir:value "25.0"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "Mutations/Megabase" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "1/1000000{Base}" ]
];
fhir:Observation.specimen [
fhir:Reference.reference [ fhir:value "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d" ]
].
<urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d> a fhir:Observation;
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant> ]
];
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p></p><p><b>category</b>: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</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=\"#urnuuidd0b4affa-91d6-46d1-af01-b30d9f16ef6d\">See above (Patient/null)</a></p><p><b>performer</b>: <a href=\"#urnuuida48256f8-db37-44e0-a0f6-d7af16c7c9ef\">See above (Practitioner/null)</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=\"#urnuuida5d6a6a9-4859-480e-85b2-56974fef3b9d\">See above (Specimen/null)</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 p.Val600Glu}\">p.Val600Glu</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 48006-1}\">Amino acid change type</span></p><p><b>value</b>: <span title=\"Codes: {http://loinc.org LA6698-0}\">Missense</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/geneId HGNC:1097}\">BRAF</span></p></blockquote></div>"
];
fhir:Observation.status [ fhir:value "final"];
fhir:Observation.category [
fhir:index 0;
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/observation-category" ];
fhir:Coding.code [ fhir:value "laboratory" ] ]
];
fhir:Observation.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:69548-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "69548-6" ];
fhir:Coding.display [ fhir:value "Genetic variant assessment" ] ]
];
fhir:Observation.subject [
fhir:Reference.reference [ fhir:value "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d" ]
];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef" ]
];
fhir:Observation.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA9633-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA9633-4" ];
fhir:Coding.display [ fhir:value "Present" ] ]
];
fhir:Observation.method [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA26398-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA26398-0" ];
fhir:Coding.display [ fhir:value "Sequencing" ] ]
];
fhir:Observation.specimen [
fhir:Reference.reference [ fhir:value "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d" ]
];
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:62374-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "62374-4" ];
fhir:Coding.display [ fhir:value "Human reference sequence assembly version" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA14029-5;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA14029-5" ];
fhir:Coding.display [ fhir:value "GRCh37" ] ] ]
], [
fhir:index 1;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81290-9;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81290-9" ];
fhir:Coding.display [ fhir:value "Genomic DNA change (gHGVS)" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.code [ fhir:value "NC_000007.13:g.140453136A>T" ];
fhir:Coding.display [ fhir:value "NC_000007.13:g.140453136A>T" ] ] ]
], [
fhir:index 2;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81252-9;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81252-9" ];
fhir:Coding.display [ fhir:value "Discrete genetic variant" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/clinvar" ];
fhir:Coding.code [ fhir:value "13961" ];
fhir:Coding.display [ fhir:value "Clinvar ID 13961" ] ] ]
], [
fhir:index 3;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48005-3;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48005-3" ];
fhir:Coding.display [ fhir:value "Amino acid change (pHGVS)" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.code [ fhir:value "p.Val600Glu" ];
fhir:Coding.display [ fhir:value "p.Val600Glu" ] ] ]
], [
fhir:index 4;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48006-1;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48006-1" ];
fhir:Coding.display [ fhir:value "Amino acid change type" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6698-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6698-0" ];
fhir:Coding.display [ fhir:value "Missense" ] ] ]
], [
fhir:index 5;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48018-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48018-6" ];
fhir:Coding.display [ fhir:value "Gene studied ID" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.genenames.org/geneId" ];
fhir:Coding.code [ fhir:value "HGNC:1097" ];
fhir:Coding.display [ fhir:value "BRAF" ] ] ]
].
<urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524> a fhir:Observation;
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication> ]
];
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "extensions" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p><b>Related 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>"
];
fhir:DomainResource.extension [
fhir:index 0;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/CGRelatedArtifact" ];
fhir:Extension.valueRelatedArtifact [
fhir:RelatedArtifact.type [ fhir:value "justification" ];
fhir:RelatedArtifact.display [ fhir:value "https://pmkb.weill.cornell.edu/therapies/103" ] ]
];
fhir:Observation.status [ fhir:value "final"];
fhir:Observation.category [
fhir:index 0;
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/observation-category" ];
fhir:Coding.code [ fhir:value "laboratory" ] ]
];
fhir:Observation.code [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes" ];
fhir:Coding.code [ fhir:value "diagnostic-implication" ];
fhir:Coding.display [ fhir:value "Diagnostic Implication" ] ]
];
fhir:Observation.subject [
fhir:Reference.reference [ fhir:value "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d" ]
];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef" ]
];
fhir:Observation.method [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA26811-2;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA26811-2" ];
fhir:Coding.display [ fhir:value "Computational analysis" ] ]
];
fhir:Observation.specimen [
fhir:Reference.reference [ fhir:value "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d" ]
];
fhir:Observation.derivedFrom [
fhir:index 0;
fhir:Reference.reference [ fhir:value "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d" ]
];
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:53037-8;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "53037-8" ];
fhir:Coding.display [ fhir:value "Genetic variation clinical significance [Imp]" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6668-3;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6668-3" ];
fhir:Coding.display [ fhir:value "Pathogenic" ] ] ]
], [
fhir:index 1;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:93044-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "93044-6" ];
fhir:Coding.display [ fhir:value "Level of Evidence" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA30200-2;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA30200-2" ];
fhir:Coding.display [ fhir:value "Very strong evidence pathogenic" ] ] ]
], [
fhir:index 2;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes" ];
fhir:Coding.code [ fhir:value "associated-cancer" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.text [ fhir:value "melanoma" ] ]
].
<urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5> a fhir:DiagnosticReport;
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report> ]
];
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p><b>status</b>: final</p><p><b>category</b>: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 81247-9}\">Genetic analysis report</span></p><p><b>subject</b>: <a href=\"#urnuuidd0b4affa-91d6-46d1-af01-b30d9f16ef6d\">See above (Patient/null)</a></p><p><b>performer</b>: <a href=\"#urnuuida48256f8-db37-44e0-a0f6-d7af16c7c9ef\">See above (Practitioner/null)</a></p><p><b>specimen</b>: <a href=\"#urnuuida5d6a6a9-4859-480e-85b2-56974fef3b9d\">See above (Specimen/null)</a></p><p><b>result</b>: </p><ul><li><a href=\"#urnuuid16fdd5fc-e665-48af-99e4-48d603f3e12d\">BRAF V600E mutation observed. Generated Summary: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>; <span title=\"Codes: {http://loinc.org 69548-6}\">Genetic variant assessment</span>; <span title=\"Codes: {http://loinc.org LA9633-4}\">Present</span>; <span title=\"Codes: {http://loinc.org LA26398-0}\">Sequencing</span></a></li><li><a href=\"#urnuuid1bf9642d-fd1c-4819-8c5d-44fae4bad524\">melanoma implicated. Generated Summary: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>; <span title=\"Codes: {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes diagnostic-implication}\">Diagnostic Implication</span>; <span title=\"Codes: {http://loinc.org LA26811-2}\">Computational analysis</span></a></li></ul></div>"
];
fhir:DiagnosticReport.status [ fhir:value "final"];
fhir:DiagnosticReport.category [
fhir:index 0;
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/v2-0074" ];
fhir:Coding.code [ fhir:value "GE" ] ]
];
fhir:DiagnosticReport.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81247-9;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81247-9" ];
fhir:Coding.display [ fhir:value "Master HL7 genetic variant reporting panel" ] ];
fhir:CodeableConcept.text [ fhir:value "Genetic analysis report" ]
];
fhir:DiagnosticReport.subject [
fhir:Reference.reference [ fhir:value "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d" ]
];
fhir:DiagnosticReport.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef" ]
];
fhir:DiagnosticReport.specimen [
fhir:index 0;
fhir:Reference.reference [ fhir:value "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d" ]
];
fhir:DiagnosticReport.result [
fhir:index 0;
fhir:Reference.reference [ fhir:value "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d" ];
fhir:Reference.display [ fhir:value "BRAF V600E mutation observed" ]
], [
fhir:index 1;
fhir:Reference.reference [ fhir:value "urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524" ];
fhir:Reference.display [ fhir:value "melanoma implicated" ]
].
# - ontology header ------------------------------------------------------------
a owl:Ontology;
owl:imports fhir:fhir.ttl.
IG © 2019+ HL7 International Clinical Genomics Work Group. Package hl7.fhir.uv.genomics-reporting#1.1.0 based on FHIR 4.0.1. Generated 2021-04-13
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