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 in its permanent home (it will always be available at this URL). 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 "bundle-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:Resource.id [ fhir:value "Inline-Instance-for-oncology-diagnostic-1"];
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><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>"
];
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:Resource.id [ fhir:value "Inline-Instance-for-oncology-diagnostic-2"];
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><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>"
];
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.id [ fhir:value "Inline-Instance-for-oncology-diagnostic-3"];
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><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>"
];
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:Resource.id [ fhir:value "Inline-Instance-for-oncology-diagnostic-4"];
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><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>"
];
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"^^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.id [ fhir:value "Inline-Instance-for-oncology-diagnostic-5"];
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><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>"
];
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.id [ fhir:value "Inline-Instance-for-oncology-diagnostic-6"];
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><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>"
];
fhir:DomainResource.extension [
fhir:index 0;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-artifact" ];
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/tbd-codes-cs" ];
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;
a loinc:81259-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81259-4" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.text [ fhir:value "melanoma" ] ]
].
<urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5> a fhir:DiagnosticReport;
fhir:Resource.id [ fhir:value "Inline-Instance-for-oncology-diagnostic-7"];
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><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>"
];
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 © 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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