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 
@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-report-example"];
fhir:Bundle.type [ fhir:value "transaction"];
fhir:Bundle.entry [
fhir:index 0;
fhir:Bundle.entry.fullUrl [ fhir:value "urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17" ];
fhir:Bundle.entry.resource <urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Organization" ];
fhir:Bundle.entry.request.ifNoneExist [ fhir:value "identifier=http://molit.eu/fhir/genomics/NamingSystem/organization|CEGAT" ] ]
], [
fhir:index 1;
fhir:Bundle.entry.fullUrl [ fhir:value "urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648" ];
fhir:Bundle.entry.resource <urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Patient" ];
fhir:Bundle.entry.request.ifNoneExist [ fhir:value "identifier=http://molit.eu/fhir/genomics/NamingSystem/cegat/patID|11111" ] ]
], [
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fhir:Bundle.entry.fullUrl [ fhir:value "urn:uuid:a2041c83-b73d-4fc8-9466-4ba4a92da516" ];
fhir:Bundle.entry.resource <urn:uuid:a2041c83-b73d-4fc8-9466-4ba4a92da516>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Specimen" ];
fhir:Bundle.entry.request.ifNoneExist [ fhir:value "identifier=http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID|UNKNOWN" ] ]
], [
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fhir:Bundle.entry.fullUrl [ fhir:value "urn:uuid:dac358c3-403a-4dbb-b478-4259aed882ae" ];
fhir:Bundle.entry.resource <urn:uuid:dac358c3-403a-4dbb-b478-4259aed882ae>;
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fhir:Bundle.entry.resource <urn:uuid:842d9ab9-d940-4f0c-adf9-e5c528f5c0e5>;
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fhir:Bundle.entry.resource <urn:uuid:58828523-8893-45fc-973b-16290366c5e5>;
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fhir:Bundle.entry.resource <urn:uuid:2c28b23f-3e9f-4c03-8c8f-0e76bc5dc9c2>;
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fhir:Bundle.entry.resource <urn:uuid:41bebbe5-e06f-4867-aa22-7c06db69dbd1>;
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fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ]
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fhir:Bundle.entry.resource <urn:uuid:c3587931-242f-4129-93f9-be24500c8f29>;
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fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ]
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fhir:Bundle.entry.fullUrl [ fhir:value "urn:uuid:41695fc0-1fd5-4cc8-95e6-82b2848a5cb6" ];
fhir:Bundle.entry.resource <urn:uuid:41695fc0-1fd5-4cc8-95e6-82b2848a5cb6>;
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fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ]
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fhir:Bundle.entry.fullUrl [ fhir:value "urn:uuid:58eb14f6-4059-4168-86a9-155ae61d30e2" ];
fhir:Bundle.entry.resource <urn:uuid:58eb14f6-4059-4168-86a9-155ae61d30e2>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ]
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fhir:Bundle.entry.fullUrl [ fhir:value "urn:uuid:1a71e80f-b044-4a91-80e1-eadbe5a53dca" ];
fhir:Bundle.entry.resource <urn:uuid:1a71e80f-b044-4a91-80e1-eadbe5a53dca>;
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fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ]
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fhir:Bundle.entry.fullUrl [ fhir:value "urn:uuid:6a80003f-822d-489e-8286-1f1dcba56dfa" ];
fhir:Bundle.entry.resource <urn:uuid:6a80003f-822d-489e-8286-1f1dcba56dfa>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "DiagnosticReport" ] ]
].
<urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17> a fhir:Organization;
fhir:Resource.id [ fhir:value "Inline-Instance-for-oncology-report-example-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-report-example-1\" </p></div><p><b>identifier</b>: id: CEGAT</p><p><b>name</b>: CEGAT</p></div>"
];
fhir:Organization.identifier [
fhir:index 0;
fhir:Identifier.system [ fhir:value "http://molit.eu/fhir/genomics/NamingSystem/organization" ];
fhir:Identifier.value [ fhir:value "CEGAT" ]
];
fhir:Organization.name [ fhir:value "CEGAT"].
<urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648> a fhir:Patient;
fhir:Resource.id [ fhir:value "Inline-Instance-for-oncology-report-example-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-report-example-2\" </p></div><p><b>identifier</b>: id: 11111</p></div>"
];
fhir:Patient.identifier [
fhir:index 0;
fhir:Identifier.system [ fhir:value "http://molit.eu/fhir/genomics/NamingSystem/cegat/patID" ];
fhir:Identifier.value [ fhir:value "11111" ]
].
<urn:uuid:a2041c83-b73d-4fc8-9466-4ba4a92da516> a fhir:Specimen;
fhir:Resource.id [ fhir:value "Inline-Instance-for-oncology-report-example-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-report-example-3\" </p></div><p><b>identifier</b>: id: UNKNOWN</p><p><b>type</b>: Tumor <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v2-0487.html\">specimenType</a>#TUMOR)</span></p><p><b>subject</b>: <a href=\"#Patient_Inline-Instance-for-oncology-report-example-2\">See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)</a></p><h3>Collections</h3><table class=\"grid\"><tr><td>-</td><td><b>Method</b></td><td><b>BodySite</b></td></tr><tr><td>*</td><td>Biopsy <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> ()</span></td><td>Malignant neoplasm of cardia <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-icd10CM.html\">International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM)</a>#C16.0)</span></td></tr></table></div>"
];
fhir:Specimen.identifier [
fhir:index 0;
fhir:Identifier.system [ fhir:value "http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID" ];
fhir:Identifier.value [ fhir:value "UNKNOWN" ]
];
fhir:Specimen.type [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/v2-0487" ];
fhir:Coding.code [ fhir:value "TUMOR" ];
fhir:Coding.display [ fhir:value "Tumor" ] ]
];
fhir:Specimen.subject [
fhir:Reference.reference [ fhir:value "urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648" ]
];
fhir:Specimen.collection [
fhir:Specimen.collection.method [
fhir:CodeableConcept.text [ fhir:value "Biopsy" ] ];
fhir:Specimen.collection.bodySite [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://hl7.org/fhir/sid/icd-10-cm" ];
fhir:Coding.code [ fhir:value "C16.0" ] ] ]
].
<urn:uuid:dac358c3-403a-4dbb-b478-4259aed882ae> a fhir:Observation;
fhir:Resource.id [ fhir:value "Inline-Instance-for-oncology-report-example-4"];
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-report-example-4\" </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-report-example-2\">See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)</a></p><p><b>performer</b>: <a href=\"#Organization_Inline-Instance-for-oncology-report-example-1\">See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)</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>: <span></span></p><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48002-0)</span></p><p><b>value</b>: Somatic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6684-0)</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>: PIK3CA <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#HGNC:8975)</span></p></blockquote><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>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: c.3140A>G <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>#c.3140A>G)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48019-4)</span></p><p><b>value</b>: substitution <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:1000002)</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.H1047R <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.H1047R)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Molecular Consequence <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#molecular-consequence)</span></p><p><b>value</b>: missense_variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:0001583)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_006218.3 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_006218.3)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic ref allele [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69547-8)</span></p><p><b>value</b>: A</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample VAF <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81258-6)</span></p><p><b>value</b>: 0.2188 relative frequency of a particular allele in the specimen<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic read depth <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#82121-5)</span></p><p><b>value</b>: 64 reads per base pair<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code {reads}/{base} = '{reads}/{base}')</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:f7a438e6-f484-453d-97e8-aa4d51008648" ]
];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17" ]
];
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.identifier [
fhir:Identifier.system [ fhir:value "http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID" ];
fhir:Identifier.value [ fhir:value "UNKNOWN" ] ]
];
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48002-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48002-0" ];
fhir:Coding.display [ fhir:value "Genomic source class" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6684-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6684-0" ];
fhir:Coding.display [ fhir:value "Somatic" ] ] ]
], [
fhir:index 1;
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:8975" ];
fhir:Coding.display [ fhir:value "PIK3CA" ] ] ]
], [
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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 3;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48004-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48004-6" ];
fhir:Coding.display [ fhir:value "DNA change (c.HGVS)" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.code [ fhir:value "c.3140A>G" ];
fhir:Coding.display [ fhir:value "c.3140A>G" ] ] ]
], [
fhir:index 4;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48019-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48019-4" ];
fhir:Coding.display [ fhir:value "DNA change type" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:1000002" ];
fhir:Coding.display [ fhir:value "substitution" ] ] ]
], [
fhir:index 5;
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.H1047R" ];
fhir:Coding.display [ fhir:value "p.H1047R" ] ] ]
], [
fhir:index 6;
fhir:Observation.component.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 "molecular-consequence" ];
fhir:Coding.display [ fhir:value "Molecular Consequence" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:0001583" ];
fhir:Coding.display [ fhir:value "missense_variant" ] ] ]
], [
fhir:index 7;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:51958-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "51958-7" ];
fhir:Coding.display [ fhir:value "Transcript reference sequence [ID]" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ];
fhir:Coding.code [ fhir:value "NM_006218.3" ];
fhir:Coding.display [ fhir:value "NM_006218.3" ] ] ]
], [
fhir:index 8;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:69547-8;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "69547-8" ];
fhir:Coding.display [ fhir:value "Genomic ref allele [ID]" ] ] ];
fhir:Observation.component.valueString [ fhir:value "A" ]
], [
fhir:index 9;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81258-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81258-6" ];
fhir:Coding.display [ fhir:value "Sample VAF" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "0.2188"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "relative frequency of a particular allele in the specimen" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "1" ] ]
], [
fhir:index 10;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:82121-5;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "82121-5" ];
fhir:Coding.display [ fhir:value "Allelic read depth" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "64"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "reads per base pair" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "{reads}/{base}" ] ]
].
<urn:uuid:1d773d66-cec7-44a2-b92a-46d00adeae00> a fhir:Observation;
fhir:Resource.id [ fhir:value "Inline-Instance-for-oncology-report-example-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-report-example-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-report-example-2\">See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)</a></p><p><b>performer</b>: <a href=\"#Organization_Inline-Instance-for-oncology-report-example-1\">See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)</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>: <span></span></p><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48002-0)</span></p><p><b>value</b>: Somatic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6684-0)</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>: NRAS <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#HGNC:7989)</span></p></blockquote><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>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: c.34G>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>#c.34G>T)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48019-4)</span></p><p><b>value</b>: substitution <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:1000002)</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.G12C <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.G12C)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Molecular Consequence <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#molecular-consequence)</span></p><p><b>value</b>: missense_variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:0001583)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_002524.4 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_002524.4)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic ref allele [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69547-8)</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample VAF <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81258-6)</span></p><p><b>value</b>: 0.1793 relative frequency of a particular allele in the specimen<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic read depth <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#82121-5)</span></p><p><b>value</b>: 145 reads per base pair<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code {reads}/{base} = '{reads}/{base}')</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:f7a438e6-f484-453d-97e8-aa4d51008648" ]
];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17" ]
];
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.identifier [
fhir:Identifier.system [ fhir:value "http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID" ];
fhir:Identifier.value [ fhir:value "UNKNOWN" ] ]
];
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48002-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48002-0" ];
fhir:Coding.display [ fhir:value "Genomic source class" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6684-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6684-0" ];
fhir:Coding.display [ fhir:value "Somatic" ] ] ]
], [
fhir:index 1;
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:7989" ];
fhir:Coding.display [ fhir:value "NRAS" ] ] ]
], [
fhir:index 2;
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 3;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48004-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48004-6" ];
fhir:Coding.display [ fhir:value "DNA change (c.HGVS)" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.code [ fhir:value "c.34G>T" ];
fhir:Coding.display [ fhir:value "c.34G>T" ] ] ]
], [
fhir:index 4;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48019-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48019-4" ];
fhir:Coding.display [ fhir:value "DNA change type" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:1000002" ];
fhir:Coding.display [ fhir:value "substitution" ] ] ]
], [
fhir:index 5;
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.G12C" ];
fhir:Coding.display [ fhir:value "p.G12C" ] ] ]
], [
fhir:index 6;
fhir:Observation.component.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 "molecular-consequence" ];
fhir:Coding.display [ fhir:value "Molecular Consequence" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:0001583" ];
fhir:Coding.display [ fhir:value "missense_variant" ] ] ]
], [
fhir:index 7;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:51958-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "51958-7" ];
fhir:Coding.display [ fhir:value "Transcript reference sequence [ID]" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ];
fhir:Coding.code [ fhir:value "NM_002524.4" ];
fhir:Coding.display [ fhir:value "NM_002524.4" ] ] ]
], [
fhir:index 8;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:69547-8;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "69547-8" ];
fhir:Coding.display [ fhir:value "Genomic ref allele [ID]" ] ] ];
fhir:Observation.component.valueString [ fhir:value "C" ]
], [
fhir:index 9;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81258-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81258-6" ];
fhir:Coding.display [ fhir:value "Sample VAF" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "0.1793"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "relative frequency of a particular allele in the specimen" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "1" ] ]
], [
fhir:index 10;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:82121-5;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "82121-5" ];
fhir:Coding.display [ fhir:value "Allelic read depth" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "145"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "reads per base pair" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "{reads}/{base}" ] ]
].
<urn:uuid:842d9ab9-d940-4f0c-adf9-e5c528f5c0e5> a fhir:Observation;
fhir:Resource.id [ fhir:value "Inline-Instance-for-oncology-report-example-6"];
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-report-example-6\" </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-report-example-2\">See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)</a></p><p><b>performer</b>: <a href=\"#Organization_Inline-Instance-for-oncology-report-example-1\">See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)</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>: <span></span></p><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48002-0)</span></p><p><b>value</b>: Somatic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6684-0)</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>: FBXW7 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#HGNC:16712)</span></p></blockquote><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>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: c.1394G>A <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>#c.1394G>A)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48019-4)</span></p><p><b>value</b>: substitution <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:1000002)</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.R465H <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.R465H)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Molecular Consequence <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#molecular-consequence)</span></p><p><b>value</b>: missense_variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:0001583)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_001349798.2 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_001349798.2)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic ref allele [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69547-8)</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample VAF <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81258-6)</span></p><p><b>value</b>: 0.1053 relative frequency of a particular allele in the specimen<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic read depth <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#82121-5)</span></p><p><b>value</b>: 57 reads per base pair<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code {reads}/{base} = '{reads}/{base}')</span></p></blockquote></div>"
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fhir:Coding.display [ fhir:value "Genetic variant assessment" ] ]
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fhir:Observation.specimen [
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fhir:Coding.display [ fhir:value "Somatic" ] ] ]
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fhir:Coding.code [ fhir:value "62374-4" ];
fhir:Coding.display [ fhir:value "Human reference sequence assembly version" ] ] ];
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fhir:Coding.display [ fhir:value "GRCh37" ] ] ]
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fhir:index 0;
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fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48004-6" ];
fhir:Coding.display [ fhir:value "DNA change (c.HGVS)" ] ] ];
fhir:Observation.component.valueCodeableConcept [
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fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.code [ fhir:value "c.1394G>A" ];
fhir:Coding.display [ fhir:value "c.1394G>A" ] ] ]
], [
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fhir:Coding.display [ fhir:value "substitution" ] ] ]
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fhir:Observation.component.code [
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fhir:index 0;
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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.R465H" ];
fhir:Coding.display [ fhir:value "p.R465H" ] ] ]
], [
fhir:index 6;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" ];
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fhir:Coding.display [ fhir:value "Molecular Consequence" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
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fhir:Coding.display [ fhir:value "missense_variant" ] ] ]
], [
fhir:index 7;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:51958-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "51958-7" ];
fhir:Coding.display [ fhir:value "Transcript reference sequence [ID]" ] ] ];
fhir:Observation.component.valueCodeableConcept [
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fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ];
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fhir:Coding.display [ fhir:value "NM_001349798.2" ] ] ]
], [
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fhir:Observation.component.code [
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fhir:index 0;
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fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "69547-8" ];
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fhir:Observation.component.valueString [ fhir:value "C" ]
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fhir:index 0;
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fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81258-6" ];
fhir:Coding.display [ fhir:value "Sample VAF" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "0.1053"^^xsd:decimal ];
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fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "1" ] ]
], [
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fhir:Observation.component.code [
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fhir:index 0;
a loinc:82121-5;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "82121-5" ];
fhir:Coding.display [ fhir:value "Allelic read depth" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "57"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "reads per base pair" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "{reads}/{base}" ] ]
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<urn:uuid:9a9f9a4a-52e3-4738-bd0b-a25374bbf358> a fhir:Observation;
fhir:Resource.id [ fhir:value "Inline-Instance-for-oncology-report-example-7"];
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> ]
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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-report-example-7\" </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-report-example-2\">See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)</a></p><p><b>performer</b>: <a href=\"#Organization_Inline-Instance-for-oncology-report-example-1\">See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)</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>: <span></span></p><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48002-0)</span></p><p><b>value</b>: Somatic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6684-0)</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>: KMT2D <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#HGNC:7133)</span></p></blockquote><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>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: c.7900_7901delCA <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>#c.7900_7901delCA)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48019-4)</span></p><p><b>value</b>: deletion <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:0000159)</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.Q2634Afs*20 <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.Q2634Afs*20)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Molecular Consequence <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#molecular-consequence)</span></p><p><b>value</b>: frameshift <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:0000865)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_003482.3 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_003482.3)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic ref allele [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69547-8)</span></p><p><b>value</b>: CTG</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample VAF <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81258-6)</span></p><p><b>value</b>: 0.188 relative frequency of a particular allele in the specimen<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic read depth <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#82121-5)</span></p><p><b>value</b>: 117 reads per base pair<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code {reads}/{base} = '{reads}/{base}')</span></p></blockquote></div>"
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fhir:Coding.display [ fhir:value "Genetic variant assessment" ] ]
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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;
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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.identifier [
fhir:Identifier.system [ fhir:value "http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID" ];
fhir:Identifier.value [ fhir:value "UNKNOWN" ] ]
];
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48002-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48002-0" ];
fhir:Coding.display [ fhir:value "Genomic source class" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6684-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6684-0" ];
fhir:Coding.display [ fhir:value "Somatic" ] ] ]
], [
fhir:index 1;
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:7133" ];
fhir:Coding.display [ fhir:value "KMT2D" ] ] ]
], [
fhir:index 2;
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 3;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48004-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48004-6" ];
fhir:Coding.display [ fhir:value "DNA change (c.HGVS)" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.code [ fhir:value "c.7900_7901delCA" ];
fhir:Coding.display [ fhir:value "c.7900_7901delCA" ] ] ]
], [
fhir:index 4;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48019-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48019-4" ];
fhir:Coding.display [ fhir:value "DNA change type" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:0000159" ];
fhir:Coding.display [ fhir:value "deletion" ] ] ]
], [
fhir:index 5;
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.Q2634Afs*20" ];
fhir:Coding.display [ fhir:value "p.Q2634Afs*20" ] ] ]
], [
fhir:index 6;
fhir:Observation.component.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 "molecular-consequence" ];
fhir:Coding.display [ fhir:value "Molecular Consequence" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:0000865" ];
fhir:Coding.display [ fhir:value "frameshift" ] ] ]
], [
fhir:index 7;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:51958-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "51958-7" ];
fhir:Coding.display [ fhir:value "Transcript reference sequence [ID]" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ];
fhir:Coding.code [ fhir:value "NM_003482.3" ];
fhir:Coding.display [ fhir:value "NM_003482.3" ] ] ]
], [
fhir:index 8;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:69547-8;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "69547-8" ];
fhir:Coding.display [ fhir:value "Genomic ref allele [ID]" ] ] ];
fhir:Observation.component.valueString [ fhir:value "CTG" ]
], [
fhir:index 9;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81258-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81258-6" ];
fhir:Coding.display [ fhir:value "Sample VAF" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "0.188"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "relative frequency of a particular allele in the specimen" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "1" ] ]
], [
fhir:index 10;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:82121-5;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "82121-5" ];
fhir:Coding.display [ fhir:value "Allelic read depth" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "117"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "reads per base pair" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "{reads}/{base}" ] ]
].
<urn:uuid:58828523-8893-45fc-973b-16290366c5e5> a fhir:Observation;
fhir:Resource.id [ fhir:value "Inline-Instance-for-oncology-report-example-8"];
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-report-example-8\" </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-report-example-2\">See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)</a></p><p><b>performer</b>: <a href=\"#Organization_Inline-Instance-for-oncology-report-example-1\">See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)</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>: <span></span></p><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48002-0)</span></p><p><b>value</b>: Somatic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6684-0)</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>: PIK3CA <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#HGNC:8975)</span></p></blockquote><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>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: c.333G>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>#c.333G>T)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48019-4)</span></p><p><b>value</b>: substitution <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:1000002)</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.K111N <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.K111N)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Molecular Consequence <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#molecular-consequence)</span></p><p><b>value</b>: missense_variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:0001583)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_006218.3 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_006218.3)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic ref allele [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69547-8)</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample VAF <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81258-6)</span></p><p><b>value</b>: 0.1471 relative frequency of a particular allele in the specimen<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic read depth <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#82121-5)</span></p><p><b>value</b>: 68 reads per base pair<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code {reads}/{base} = '{reads}/{base}')</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:f7a438e6-f484-453d-97e8-aa4d51008648" ]
];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17" ]
];
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.identifier [
fhir:Identifier.system [ fhir:value "http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID" ];
fhir:Identifier.value [ fhir:value "UNKNOWN" ] ]
];
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48002-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48002-0" ];
fhir:Coding.display [ fhir:value "Genomic source class" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6684-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6684-0" ];
fhir:Coding.display [ fhir:value "Somatic" ] ] ]
], [
fhir:index 1;
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:8975" ];
fhir:Coding.display [ fhir:value "PIK3CA" ] ] ]
], [
fhir:index 2;
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 3;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48004-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48004-6" ];
fhir:Coding.display [ fhir:value "DNA change (c.HGVS)" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.code [ fhir:value "c.333G>T" ];
fhir:Coding.display [ fhir:value "c.333G>T" ] ] ]
], [
fhir:index 4;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48019-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48019-4" ];
fhir:Coding.display [ fhir:value "DNA change type" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:1000002" ];
fhir:Coding.display [ fhir:value "substitution" ] ] ]
], [
fhir:index 5;
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.K111N" ];
fhir:Coding.display [ fhir:value "p.K111N" ] ] ]
], [
fhir:index 6;
fhir:Observation.component.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 "molecular-consequence" ];
fhir:Coding.display [ fhir:value "Molecular Consequence" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:0001583" ];
fhir:Coding.display [ fhir:value "missense_variant" ] ] ]
], [
fhir:index 7;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:51958-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "51958-7" ];
fhir:Coding.display [ fhir:value "Transcript reference sequence [ID]" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ];
fhir:Coding.code [ fhir:value "NM_006218.3" ];
fhir:Coding.display [ fhir:value "NM_006218.3" ] ] ]
], [
fhir:index 8;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:69547-8;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "69547-8" ];
fhir:Coding.display [ fhir:value "Genomic ref allele [ID]" ] ] ];
fhir:Observation.component.valueString [ fhir:value "G" ]
], [
fhir:index 9;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81258-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81258-6" ];
fhir:Coding.display [ fhir:value "Sample VAF" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "0.1471"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "relative frequency of a particular allele in the specimen" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "1" ] ]
], [
fhir:index 10;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:82121-5;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "82121-5" ];
fhir:Coding.display [ fhir:value "Allelic read depth" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "68"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "reads per base pair" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "{reads}/{base}" ] ]
].
<urn:uuid:2c28b23f-3e9f-4c03-8c8f-0e76bc5dc9c2> a fhir:Observation;
fhir:Resource.id [ fhir:value "Inline-Instance-for-oncology-report-example-9"];
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-report-example-9\" </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-report-example-2\">See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)</a></p><p><b>performer</b>: <a href=\"#Organization_Inline-Instance-for-oncology-report-example-1\">See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)</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>: <span></span></p><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48002-0)</span></p><p><b>value</b>: Somatic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6684-0)</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>: IRS2 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#HGNC:6126)</span></p></blockquote><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>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: c.3960C>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>#c.3960C>T)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48019-4)</span></p><p><b>value</b>: substitution <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:1000002)</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.= <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.=)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Molecular Consequence <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#molecular-consequence)</span></p><p><b>value</b>: synonymous_variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:0001819)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_003749.2 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_003749.2)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic ref allele [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69547-8)</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample VAF <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81258-6)</span></p><p><b>value</b>: 0.1343 relative frequency of a particular allele in the specimen<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic read depth <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#82121-5)</span></p><p><b>value</b>: 134 reads per base pair<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code {reads}/{base} = '{reads}/{base}')</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:f7a438e6-f484-453d-97e8-aa4d51008648" ]
];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17" ]
];
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.identifier [
fhir:Identifier.system [ fhir:value "http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID" ];
fhir:Identifier.value [ fhir:value "UNKNOWN" ] ]
];
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48002-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48002-0" ];
fhir:Coding.display [ fhir:value "Genomic source class" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6684-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6684-0" ];
fhir:Coding.display [ fhir:value "Somatic" ] ] ]
], [
fhir:index 1;
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:6126" ];
fhir:Coding.display [ fhir:value "IRS2" ] ] ]
], [
fhir:index 2;
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 3;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48004-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48004-6" ];
fhir:Coding.display [ fhir:value "DNA change (c.HGVS)" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.code [ fhir:value "c.3960C>T" ];
fhir:Coding.display [ fhir:value "c.3960C>T" ] ] ]
], [
fhir:index 4;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48019-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48019-4" ];
fhir:Coding.display [ fhir:value "DNA change type" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:1000002" ];
fhir:Coding.display [ fhir:value "substitution" ] ] ]
], [
fhir:index 5;
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.=" ];
fhir:Coding.display [ fhir:value "p.=" ] ] ]
], [
fhir:index 6;
fhir:Observation.component.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 "molecular-consequence" ];
fhir:Coding.display [ fhir:value "Molecular Consequence" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:0001819" ];
fhir:Coding.display [ fhir:value "synonymous_variant" ] ] ]
], [
fhir:index 7;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:51958-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "51958-7" ];
fhir:Coding.display [ fhir:value "Transcript reference sequence [ID]" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ];
fhir:Coding.code [ fhir:value "NM_003749.2" ];
fhir:Coding.display [ fhir:value "NM_003749.2" ] ] ]
], [
fhir:index 8;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:69547-8;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "69547-8" ];
fhir:Coding.display [ fhir:value "Genomic ref allele [ID]" ] ] ];
fhir:Observation.component.valueString [ fhir:value "G" ]
], [
fhir:index 9;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81258-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81258-6" ];
fhir:Coding.display [ fhir:value "Sample VAF" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "0.1343"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "relative frequency of a particular allele in the specimen" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "1" ] ]
], [
fhir:index 10;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:82121-5;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "82121-5" ];
fhir:Coding.display [ fhir:value "Allelic read depth" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "134"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "reads per base pair" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "{reads}/{base}" ] ]
].
<urn:uuid:41bebbe5-e06f-4867-aa22-7c06db69dbd1> a fhir:Observation;
fhir:Resource.id [ fhir:value "Inline-Instance-for-oncology-report-example-10"];
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-report-example-10\" </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-report-example-2\">See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)</a></p><p><b>performer</b>: <a href=\"#Organization_Inline-Instance-for-oncology-report-example-1\">See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)</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>: <span></span></p><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48002-0)</span></p><p><b>value</b>: Somatic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6684-0)</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>: CDKN2A <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#HGNC:1787)</span></p></blockquote><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>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: c.9_32del <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>#c.9_32del)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48019-4)</span></p><p><b>value</b>: deletion <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:0000159)</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.A4_P11del <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.A4_P11del)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Molecular Consequence <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#molecular-consequence)</span></p><p><b>value</b>: inframe_variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:0001650)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_000077.4 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_000077.4)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic ref allele [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69547-8)</span></p><p><b>value</b>: AGGCTCCATGCTGCTCCCCGCCGCC</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample VAF <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81258-6)</span></p><p><b>value</b>: 0.0536 relative frequency of a particular allele in the specimen<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic read depth <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#82121-5)</span></p><p><b>value</b>: 112 reads per base pair<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code {reads}/{base} = '{reads}/{base}')</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;
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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:f7a438e6-f484-453d-97e8-aa4d51008648" ]
];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17" ]
];
fhir:Observation.valueCodeableConcept [
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fhir:index 0;
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fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA9633-4" ];
fhir:Coding.display [ fhir:value "Present" ] ]
];
fhir:Observation.method [
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fhir:index 0;
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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.identifier [
fhir:Identifier.system [ fhir:value "http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID" ];
fhir:Identifier.value [ fhir:value "UNKNOWN" ] ]
];
fhir:Observation.component [
fhir:index 0;
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fhir:index 0;
a loinc:48002-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48002-0" ];
fhir:Coding.display [ fhir:value "Genomic source class" ] ] ];
fhir:Observation.component.valueCodeableConcept [
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fhir:index 0;
a loinc:LA6684-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6684-0" ];
fhir:Coding.display [ fhir:value "Somatic" ] ] ]
], [
fhir:index 1;
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:1787" ];
fhir:Coding.display [ fhir:value "CDKN2A" ] ] ]
], [
fhir:index 2;
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 3;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48004-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48004-6" ];
fhir:Coding.display [ fhir:value "DNA change (c.HGVS)" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.code [ fhir:value "c.9_32del" ];
fhir:Coding.display [ fhir:value "c.9_32del" ] ] ]
], [
fhir:index 4;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48019-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48019-4" ];
fhir:Coding.display [ fhir:value "DNA change type" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:0000159" ];
fhir:Coding.display [ fhir:value "deletion" ] ] ]
], [
fhir:index 5;
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.A4_P11del" ];
fhir:Coding.display [ fhir:value "p.A4_P11del" ] ] ]
], [
fhir:index 6;
fhir:Observation.component.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 "molecular-consequence" ];
fhir:Coding.display [ fhir:value "Molecular Consequence" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:0001650" ];
fhir:Coding.display [ fhir:value "inframe_variant" ] ] ]
], [
fhir:index 7;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:51958-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "51958-7" ];
fhir:Coding.display [ fhir:value "Transcript reference sequence [ID]" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ];
fhir:Coding.code [ fhir:value "NM_000077.4" ];
fhir:Coding.display [ fhir:value "NM_000077.4" ] ] ]
], [
fhir:index 8;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:69547-8;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "69547-8" ];
fhir:Coding.display [ fhir:value "Genomic ref allele [ID]" ] ] ];
fhir:Observation.component.valueString [ fhir:value "AGGCTCCATGCTGCTCCCCGCCGCC" ]
], [
fhir:index 9;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81258-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81258-6" ];
fhir:Coding.display [ fhir:value "Sample VAF" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "0.0536"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "relative frequency of a particular allele in the specimen" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "1" ] ]
], [
fhir:index 10;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:82121-5;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "82121-5" ];
fhir:Coding.display [ fhir:value "Allelic read depth" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "112"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "reads per base pair" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "{reads}/{base}" ] ]
].
<urn:uuid:1642f190-e2c6-4999-8040-b9b2a70618bf> a fhir:Observation;
fhir:Resource.id [ fhir:value "Inline-Instance-for-oncology-report-example-11"];
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-report-example-11\" </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-report-example-2\">See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)</a></p><p><b>performer</b>: <a href=\"#Organization_Inline-Instance-for-oncology-report-example-1\">See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)</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>: <span></span></p><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48002-0)</span></p><p><b>value</b>: Somatic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6684-0)</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>: RECQL4 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#HGNC:9949)</span></p></blockquote><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>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: c.2086C>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>#c.2086C>T)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48019-4)</span></p><p><b>value</b>: substitution <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:1000002)</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.R696C <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.R696C)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Molecular Consequence <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#molecular-consequence)</span></p><p><b>value</b>: missense_variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:0001583)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_004260.3 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_004260.3)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic ref allele [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69547-8)</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample VAF <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81258-6)</span></p><p><b>value</b>: 0.2568 relative frequency of a particular allele in the specimen<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic read depth <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#82121-5)</span></p><p><b>value</b>: 148 reads per base pair<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code {reads}/{base} = '{reads}/{base}')</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:f7a438e6-f484-453d-97e8-aa4d51008648" ]
];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17" ]
];
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.identifier [
fhir:Identifier.system [ fhir:value "http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID" ];
fhir:Identifier.value [ fhir:value "UNKNOWN" ] ]
];
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48002-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48002-0" ];
fhir:Coding.display [ fhir:value "Genomic source class" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6684-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6684-0" ];
fhir:Coding.display [ fhir:value "Somatic" ] ] ]
], [
fhir:index 1;
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:9949" ];
fhir:Coding.display [ fhir:value "RECQL4" ] ] ]
], [
fhir:index 2;
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 3;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48004-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48004-6" ];
fhir:Coding.display [ fhir:value "DNA change (c.HGVS)" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.code [ fhir:value "c.2086C>T" ];
fhir:Coding.display [ fhir:value "c.2086C>T" ] ] ]
], [
fhir:index 4;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48019-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48019-4" ];
fhir:Coding.display [ fhir:value "DNA change type" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:1000002" ];
fhir:Coding.display [ fhir:value "substitution" ] ] ]
], [
fhir:index 5;
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.R696C" ];
fhir:Coding.display [ fhir:value "p.R696C" ] ] ]
], [
fhir:index 6;
fhir:Observation.component.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 "molecular-consequence" ];
fhir:Coding.display [ fhir:value "Molecular Consequence" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:0001583" ];
fhir:Coding.display [ fhir:value "missense_variant" ] ] ]
], [
fhir:index 7;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:51958-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "51958-7" ];
fhir:Coding.display [ fhir:value "Transcript reference sequence [ID]" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ];
fhir:Coding.code [ fhir:value "NM_004260.3" ];
fhir:Coding.display [ fhir:value "NM_004260.3" ] ] ]
], [
fhir:index 8;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:69547-8;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "69547-8" ];
fhir:Coding.display [ fhir:value "Genomic ref allele [ID]" ] ] ];
fhir:Observation.component.valueString [ fhir:value "G" ]
], [
fhir:index 9;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81258-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81258-6" ];
fhir:Coding.display [ fhir:value "Sample VAF" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "0.2568"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "relative frequency of a particular allele in the specimen" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "1" ] ]
], [
fhir:index 10;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:82121-5;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "82121-5" ];
fhir:Coding.display [ fhir:value "Allelic read depth" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "148"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "reads per base pair" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "{reads}/{base}" ] ]
].
<urn:uuid:c3587931-242f-4129-93f9-be24500c8f29> a fhir:Observation;
fhir:Resource.id [ fhir:value "Inline-Instance-for-oncology-report-example-12"];
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-report-example-12\" </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-report-example-2\">See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)</a></p><p><b>performer</b>: <a href=\"#Organization_Inline-Instance-for-oncology-report-example-1\">See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)</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>: <span></span></p><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48002-0)</span></p><p><b>value</b>: Somatic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6684-0)</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>: RYR1 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#HGNC:10483)</span></p></blockquote><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>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: c.4964G>A <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>#c.4964G>A)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48019-4)</span></p><p><b>value</b>: substitution <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:1000002)</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.R1655H <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.R1655H)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Molecular Consequence <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#molecular-consequence)</span></p><p><b>value</b>: missense_variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:0001583)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_000540.2 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_000540.2)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic ref allele [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69547-8)</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample VAF <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81258-6)</span></p><p><b>value</b>: 0.2151 relative frequency of a particular allele in the specimen<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic read depth <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#82121-5)</span></p><p><b>value</b>: 93 reads per base pair<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code {reads}/{base} = '{reads}/{base}')</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:f7a438e6-f484-453d-97e8-aa4d51008648" ]
];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17" ]
];
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.identifier [
fhir:Identifier.system [ fhir:value "http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID" ];
fhir:Identifier.value [ fhir:value "UNKNOWN" ] ]
];
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48002-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48002-0" ];
fhir:Coding.display [ fhir:value "Genomic source class" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6684-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6684-0" ];
fhir:Coding.display [ fhir:value "Somatic" ] ] ]
], [
fhir:index 1;
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:10483" ];
fhir:Coding.display [ fhir:value "RYR1" ] ] ]
], [
fhir:index 2;
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 3;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48004-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48004-6" ];
fhir:Coding.display [ fhir:value "DNA change (c.HGVS)" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.code [ fhir:value "c.4964G>A" ];
fhir:Coding.display [ fhir:value "c.4964G>A" ] ] ]
], [
fhir:index 4;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48019-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48019-4" ];
fhir:Coding.display [ fhir:value "DNA change type" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:1000002" ];
fhir:Coding.display [ fhir:value "substitution" ] ] ]
], [
fhir:index 5;
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.R1655H" ];
fhir:Coding.display [ fhir:value "p.R1655H" ] ] ]
], [
fhir:index 6;
fhir:Observation.component.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 "molecular-consequence" ];
fhir:Coding.display [ fhir:value "Molecular Consequence" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:0001583" ];
fhir:Coding.display [ fhir:value "missense_variant" ] ] ]
], [
fhir:index 7;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:51958-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "51958-7" ];
fhir:Coding.display [ fhir:value "Transcript reference sequence [ID]" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ];
fhir:Coding.code [ fhir:value "NM_000540.2" ];
fhir:Coding.display [ fhir:value "NM_000540.2" ] ] ]
], [
fhir:index 8;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:69547-8;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "69547-8" ];
fhir:Coding.display [ fhir:value "Genomic ref allele [ID]" ] ] ];
fhir:Observation.component.valueString [ fhir:value "G" ]
], [
fhir:index 9;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81258-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81258-6" ];
fhir:Coding.display [ fhir:value "Sample VAF" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "0.2151"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "relative frequency of a particular allele in the specimen" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "1" ] ]
], [
fhir:index 10;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:82121-5;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "82121-5" ];
fhir:Coding.display [ fhir:value "Allelic read depth" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "93"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "reads per base pair" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "{reads}/{base}" ] ]
].
<urn:uuid:41695fc0-1fd5-4cc8-95e6-82b2848a5cb6> a fhir:Observation;
fhir:Resource.id [ fhir:value "Inline-Instance-for-oncology-report-example-13"];
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-report-example-13\" </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-report-example-2\">See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)</a></p><p><b>performer</b>: <a href=\"#Organization_Inline-Instance-for-oncology-report-example-1\">See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)</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>: <span></span></p><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48002-0)</span></p><p><b>value</b>: Somatic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6684-0)</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>: SACS <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#HGNC:10519)</span></p></blockquote><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>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: c.12118G>A <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>#c.12118G>A)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48019-4)</span></p><p><b>value</b>: substitution <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:1000002)</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.A4040T <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.A4040T)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Molecular Consequence <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#molecular-consequence)</span></p><p><b>value</b>: missense_variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:0001583)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_014363.5 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_014363.5)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic ref allele [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69547-8)</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample VAF <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81258-6)</span></p><p><b>value</b>: 0.3333 relative frequency of a particular allele in the specimen<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic read depth <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#82121-5)</span></p><p><b>value</b>: 60 reads per base pair<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code {reads}/{base} = '{reads}/{base}')</span></p></blockquote></div>"
];
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fhir:Coding.display [ fhir:value "Genetic variant assessment" ] ]
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fhir:Observation.component.code [
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fhir:Coding.display [ fhir:value "Human reference sequence assembly version" ] ] ];
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fhir:Coding.display [ fhir:value "GRCh37" ] ] ]
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fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48004-6" ];
fhir:Coding.display [ fhir:value "DNA change (c.HGVS)" ] ] ];
fhir:Observation.component.valueCodeableConcept [
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fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
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fhir:Coding.display [ fhir:value "c.12118G>A" ] ] ]
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fhir:Observation.component.code [
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fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48019-4" ];
fhir:Coding.display [ fhir:value "DNA change type" ] ] ];
fhir:Observation.component.valueCodeableConcept [
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fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:1000002" ];
fhir:Coding.display [ fhir:value "substitution" ] ] ]
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fhir:index 5;
fhir:Observation.component.code [
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fhir:index 0;
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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.A4040T" ];
fhir:Coding.display [ fhir:value "p.A4040T" ] ] ]
], [
fhir:index 6;
fhir:Observation.component.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 "molecular-consequence" ];
fhir:Coding.display [ fhir:value "Molecular Consequence" ] ] ];
fhir:Observation.component.valueCodeableConcept [
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fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:0001583" ];
fhir:Coding.display [ fhir:value "missense_variant" ] ] ]
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fhir:index 7;
fhir:Observation.component.code [
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fhir:index 0;
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fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "51958-7" ];
fhir:Coding.display [ fhir:value "Transcript reference sequence [ID]" ] ] ];
fhir:Observation.component.valueCodeableConcept [
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fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ];
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fhir:Coding.display [ fhir:value "NM_014363.5" ] ] ]
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fhir:Observation.component.code [
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fhir:index 0;
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fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "69547-8" ];
fhir:Coding.display [ fhir:value "Genomic ref allele [ID]" ] ] ];
fhir:Observation.component.valueString [ fhir:value "C" ]
], [
fhir:index 9;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
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fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81258-6" ];
fhir:Coding.display [ fhir:value "Sample VAF" ] ] ];
fhir:Observation.component.valueQuantity [
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fhir:Quantity.unit [ fhir:value "relative frequency of a particular allele in the specimen" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "1" ] ]
], [
fhir:index 10;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:82121-5;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "82121-5" ];
fhir:Coding.display [ fhir:value "Allelic read depth" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "60"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "reads per base pair" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "{reads}/{base}" ] ]
].
<urn:uuid:58eb14f6-4059-4168-86a9-155ae61d30e2> a fhir:Observation;
fhir:Resource.id [ fhir:value "Inline-Instance-for-oncology-report-example-14"];
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-report-example-14\" </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-report-example-2\">See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)</a></p><p><b>performer</b>: <a href=\"#Organization_Inline-Instance-for-oncology-report-example-1\">See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)</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>: <span></span></p><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48002-0)</span></p><p><b>value</b>: Somatic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6684-0)</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>: SLIT2 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#HGNC:11086)</span></p></blockquote><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>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: c.1290C>A <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>#c.1290C>A)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48019-4)</span></p><p><b>value</b>: substitution <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:1000002)</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.N430K <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.N430K)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Molecular Consequence <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#molecular-consequence)</span></p><p><b>value</b>: missense_variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:0001583)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_004787.3 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_004787.3)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic ref allele [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69547-8)</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample VAF <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81258-6)</span></p><p><b>value</b>: 0.2642 relative frequency of a particular allele in the specimen<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic read depth <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#82121-5)</span></p><p><b>value</b>: 53 reads per base pair<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code {reads}/{base} = '{reads}/{base}')</span></p></blockquote></div>"
];
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fhir:Coding.display [ fhir:value "Genetic variant assessment" ] ]
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fhir:Observation.specimen [
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fhir:Observation.component [
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fhir:Coding.display [ fhir:value "Genomic source class" ] ] ];
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fhir:Coding.display [ fhir:value "Somatic" ] ] ]
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fhir:Coding.display [ fhir:value "Gene studied [ID]" ] ] ];
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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 3;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48004-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48004-6" ];
fhir:Coding.display [ fhir:value "DNA change (c.HGVS)" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.code [ fhir:value "c.1290C>A" ];
fhir:Coding.display [ fhir:value "c.1290C>A" ] ] ]
], [
fhir:index 4;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48019-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48019-4" ];
fhir:Coding.display [ fhir:value "DNA change type" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:1000002" ];
fhir:Coding.display [ fhir:value "substitution" ] ] ]
], [
fhir:index 5;
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.N430K" ];
fhir:Coding.display [ fhir:value "p.N430K" ] ] ]
], [
fhir:index 6;
fhir:Observation.component.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 "molecular-consequence" ];
fhir:Coding.display [ fhir:value "Molecular Consequence" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:0001583" ];
fhir:Coding.display [ fhir:value "missense_variant" ] ] ]
], [
fhir:index 7;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:51958-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "51958-7" ];
fhir:Coding.display [ fhir:value "Transcript reference sequence [ID]" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ];
fhir:Coding.code [ fhir:value "NM_004787.3" ];
fhir:Coding.display [ fhir:value "NM_004787.3" ] ] ]
], [
fhir:index 8;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:69547-8;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "69547-8" ];
fhir:Coding.display [ fhir:value "Genomic ref allele [ID]" ] ] ];
fhir:Observation.component.valueString [ fhir:value "C" ]
], [
fhir:index 9;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81258-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81258-6" ];
fhir:Coding.display [ fhir:value "Sample VAF" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "0.2642"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "relative frequency of a particular allele in the specimen" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "1" ] ]
], [
fhir:index 10;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:82121-5;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "82121-5" ];
fhir:Coding.display [ fhir:value "Allelic read depth" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "53"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "reads per base pair" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "{reads}/{base}" ] ]
].
<urn:uuid:1a71e80f-b044-4a91-80e1-eadbe5a53dca> a fhir:Observation;
fhir:Resource.id [ fhir:value "Inline-Instance-for-oncology-report-example-15"];
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-report-example-15\" </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-report-example-2\">See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)</a></p><p><b>performer</b>: <a href=\"#Organization_Inline-Instance-for-oncology-report-example-1\">See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)</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>: <span></span></p><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48002-0)</span></p><p><b>value</b>: Somatic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6684-0)</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>: SMARCA4 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#HGNC:11100)</span></p></blockquote><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>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: c.2372C>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>#c.2372C>T)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48019-4)</span></p><p><b>value</b>: substitution <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:1000002)</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.A791V <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.A791V)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Molecular Consequence <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#molecular-consequence)</span></p><p><b>value</b>: missense_variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (sequenceontology.org#SO:0001583)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_001128849.1 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_001128849.1)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic ref allele [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69547-8)</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample VAF <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81258-6)</span></p><p><b>value</b>: 0.1938 relative frequency of a particular allele in the specimen<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic read depth <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#82121-5)</span></p><p><b>value</b>: 160 reads per base pair<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code {reads}/{base} = '{reads}/{base}')</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:f7a438e6-f484-453d-97e8-aa4d51008648" ]
];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17" ]
];
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.identifier [
fhir:Identifier.system [ fhir:value "http://molit.eu/fhir/genomics/NamingSystem/cegat/tissueID" ];
fhir:Identifier.value [ fhir:value "UNKNOWN" ] ]
];
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48002-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48002-0" ];
fhir:Coding.display [ fhir:value "Genomic source class" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6684-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6684-0" ];
fhir:Coding.display [ fhir:value "Somatic" ] ] ]
], [
fhir:index 1;
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:11100" ];
fhir:Coding.display [ fhir:value "SMARCA4" ] ] ]
], [
fhir:index 2;
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 3;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48004-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48004-6" ];
fhir:Coding.display [ fhir:value "DNA change (c.HGVS)" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.code [ fhir:value "c.2372C>T" ];
fhir:Coding.display [ fhir:value "c.2372C>T" ] ] ]
], [
fhir:index 4;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48019-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48019-4" ];
fhir:Coding.display [ fhir:value "DNA change type" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:1000002" ];
fhir:Coding.display [ fhir:value "substitution" ] ] ]
], [
fhir:index 5;
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.A791V" ];
fhir:Coding.display [ fhir:value "p.A791V" ] ] ]
], [
fhir:index 6;
fhir:Observation.component.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 "molecular-consequence" ];
fhir:Coding.display [ fhir:value "Molecular Consequence" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:0001583" ];
fhir:Coding.display [ fhir:value "missense_variant" ] ] ]
], [
fhir:index 7;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:51958-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "51958-7" ];
fhir:Coding.display [ fhir:value "Transcript reference sequence [ID]" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ];
fhir:Coding.code [ fhir:value "NM_001128849.1" ];
fhir:Coding.display [ fhir:value "NM_001128849.1" ] ] ]
], [
fhir:index 8;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:69547-8;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "69547-8" ];
fhir:Coding.display [ fhir:value "Genomic ref allele [ID]" ] ] ];
fhir:Observation.component.valueString [ fhir:value "C" ]
], [
fhir:index 9;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81258-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81258-6" ];
fhir:Coding.display [ fhir:value "Sample VAF" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "0.1938"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "relative frequency of a particular allele in the specimen" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "1" ] ]
], [
fhir:index 10;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:82121-5;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "82121-5" ];
fhir:Coding.display [ fhir:value "Allelic read depth" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "160"^^xsd:decimal ];
fhir:Quantity.unit [ fhir:value "reads per base pair" ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "{reads}/{base}" ] ]
].
<urn:uuid:6a80003f-822d-489e-8286-1f1dcba56dfa> a fhir:DiagnosticReport;
fhir:Resource.id [ fhir:value "Inline-Instance-for-oncology-report-example-16"];
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-report-example-16\" </p></div><p><b>identifier</b>: id: 42867</p><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>: Master HL7 genetic variant reporting panel <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81247-9)</span></p><p><b>subject</b>: <a href=\"#Patient_Inline-Instance-for-oncology-report-example-2\">See above (urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648)</a></p><p><b>issued</b>: Sep 15, 2019 3:35:05 PM</p><p><b>performer</b>: <a href=\"#Organization_Inline-Instance-for-oncology-report-example-1\">See above (urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17)</a></p><p><b>specimen</b>: <a href=\"#Specimen_Inline-Instance-for-oncology-report-example-3\">See above (urn:uuid:a2041c83-b73d-4fc8-9466-4ba4a92da516)</a></p><p><b>result</b>: </p><ul><li><a href=\"#Observation_Inline-Instance-for-oncology-report-example-4\">See above (urn:uuid:dac358c3-403a-4dbb-b478-4259aed882ae)</a></li><li><a href=\"#Observation_Inline-Instance-for-oncology-report-example-5\">See above (urn:uuid:1d773d66-cec7-44a2-b92a-46d00adeae00)</a></li><li><a href=\"#Observation_Inline-Instance-for-oncology-report-example-6\">See above (urn:uuid:842d9ab9-d940-4f0c-adf9-e5c528f5c0e5)</a></li><li><a href=\"#Observation_Inline-Instance-for-oncology-report-example-7\">See above (urn:uuid:9a9f9a4a-52e3-4738-bd0b-a25374bbf358)</a></li><li><a href=\"#Observation_Inline-Instance-for-oncology-report-example-8\">See above (urn:uuid:58828523-8893-45fc-973b-16290366c5e5)</a></li><li><a href=\"#Observation_Inline-Instance-for-oncology-report-example-9\">See above (urn:uuid:2c28b23f-3e9f-4c03-8c8f-0e76bc5dc9c2)</a></li><li><a href=\"#Observation_Inline-Instance-for-oncology-report-example-10\">See above (urn:uuid:41bebbe5-e06f-4867-aa22-7c06db69dbd1)</a></li><li><a href=\"#Observation_Inline-Instance-for-oncology-report-example-11\">See above (urn:uuid:1642f190-e2c6-4999-8040-b9b2a70618bf)</a></li><li><a href=\"#Observation_Inline-Instance-for-oncology-report-example-12\">See above (urn:uuid:c3587931-242f-4129-93f9-be24500c8f29)</a></li><li><a href=\"#Observation_Inline-Instance-for-oncology-report-example-13\">See above (urn:uuid:41695fc0-1fd5-4cc8-95e6-82b2848a5cb6)</a></li><li><a href=\"#Observation_Inline-Instance-for-oncology-report-example-14\">See above (urn:uuid:58eb14f6-4059-4168-86a9-155ae61d30e2)</a></li><li><a href=\"#Observation_Inline-Instance-for-oncology-report-example-15\">See above (urn:uuid:1a71e80f-b044-4a91-80e1-eadbe5a53dca)</a></li></ul></div>"
];
fhir:DiagnosticReport.identifier [
fhir:index 0;
fhir:Identifier.system [ fhir:value "http://molit.eu/fhir/genomics/NamingSystem/cegat/reportID" ];
fhir:Identifier.value [ fhir:value "42867" ]
];
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:Coding.display [ fhir:value "Genetics" ] ]
];
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:DiagnosticReport.subject [
fhir:Reference.reference [ fhir:value "urn:uuid:f7a438e6-f484-453d-97e8-aa4d51008648" ]
];
fhir:DiagnosticReport.issued [ fhir:value "2019-09-15T11:35:05.722-04:00"^^xsd:dateTime];
fhir:DiagnosticReport.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "urn:uuid:fc16d84c-8584-4e1d-baae-64e2f95bfe17" ]
];
fhir:DiagnosticReport.specimen [
fhir:index 0;
fhir:Reference.reference [ fhir:value "urn:uuid:a2041c83-b73d-4fc8-9466-4ba4a92da516" ]
];
fhir:DiagnosticReport.result [
fhir:index 0;
fhir:Reference.reference [ fhir:value "urn:uuid:dac358c3-403a-4dbb-b478-4259aed882ae" ]
], [
fhir:index 1;
fhir:Reference.reference [ fhir:value "urn:uuid:1d773d66-cec7-44a2-b92a-46d00adeae00" ]
], [
fhir:index 2;
fhir:Reference.reference [ fhir:value "urn:uuid:842d9ab9-d940-4f0c-adf9-e5c528f5c0e5" ]
], [
fhir:index 3;
fhir:Reference.reference [ fhir:value "urn:uuid:9a9f9a4a-52e3-4738-bd0b-a25374bbf358" ]
], [
fhir:index 4;
fhir:Reference.reference [ fhir:value "urn:uuid:58828523-8893-45fc-973b-16290366c5e5" ]
], [
fhir:index 5;
fhir:Reference.reference [ fhir:value "urn:uuid:2c28b23f-3e9f-4c03-8c8f-0e76bc5dc9c2" ]
], [
fhir:index 6;
fhir:Reference.reference [ fhir:value "urn:uuid:41bebbe5-e06f-4867-aa22-7c06db69dbd1" ]
], [
fhir:index 7;
fhir:Reference.reference [ fhir:value "urn:uuid:1642f190-e2c6-4999-8040-b9b2a70618bf" ]
], [
fhir:index 8;
fhir:Reference.reference [ fhir:value "urn:uuid:c3587931-242f-4129-93f9-be24500c8f29" ]
], [
fhir:index 9;
fhir:Reference.reference [ fhir:value "urn:uuid:41695fc0-1fd5-4cc8-95e6-82b2848a5cb6" ]
], [
fhir:index 10;
fhir:Reference.reference [ fhir:value "urn:uuid:58eb14f6-4059-4168-86a9-155ae61d30e2" ]
], [
fhir:index 11;
fhir:Reference.reference [ fhir:value "urn:uuid:1a71e80f-b044-4a91-80e1-eadbe5a53dca" ]
].
# - 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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