Genomics Reporting Implementation Guide
2.0.0 - trial-use
Genomics Reporting Implementation Guide
2.0.0 - trial-use
This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions 
@prefix fhir: <http://hl7.org/fhir/> .
@prefix loinc: <http://loinc.org/rdf#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix sct: <http://snomed.info/id/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
# - resource -------------------------------------------------------------------
a fhir:Bundle;
fhir:nodeRole fhir:treeRoot;
fhir:Resource.id [ fhir:value "bundle-cgexample-withGrouping"];
fhir:Bundle.type [ fhir:value "collection"];
fhir:Bundle.entry [
fhir:index 0;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/DiagnosticReport/report-withGrouping" ];
fhir:Bundle.entry.resource <http://example.org/fhir/DiagnosticReport/report-withGrouping>
], [
fhir:index 1;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Patient/ExamplePatient" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Patient/ExamplePatient>
], [
fhir:index 2;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Specimen/ExampleSpecimen" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Specimen/ExampleSpecimen>
], [
fhir:index 3;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Organization/ExampleLab" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Organization/ExampleLab>
], [
fhir:index 4;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/ServiceRequest/ExampleServiceRequest" ];
fhir:Bundle.entry.resource <http://example.org/fhir/ServiceRequest/ExampleServiceRequest>
], [
fhir:index 5;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/overall-interp-1a" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Observation/overall-interp-1a>
], [
fhir:index 6;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/discrete-variant-1a" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Observation/discrete-variant-1a>
], [
fhir:index 7;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/dis-path-1a" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Observation/dis-path-1a>
], [
fhir:index 8;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/complex-variant-1a" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Observation/complex-variant-1a>
], [
fhir:index 9;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/complex-dis-path-1a" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Observation/complex-dis-path-1a>
], [
fhir:index 10;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/complex-component-D-1a" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Observation/complex-component-D-1a>
], [
fhir:index 11;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/complex-component-E-1a" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Observation/complex-component-E-1a>
], [
fhir:index 12;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/pharmPanel-1a" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Observation/pharmPanel-1a>
], [
fhir:index 13;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/haplotype-1a" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Observation/haplotype-1a>
], [
fhir:index 14;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/genotype-1a" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Observation/genotype-1a>
], [
fhir:index 15;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/metab-1a" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Observation/metab-1a>
], [
fhir:index 16;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/efficacy-1a" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Observation/efficacy-1a>
], [
fhir:index 17;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/highrisk-1a" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Observation/highrisk-1a>
], [
fhir:index 18;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Task/usage-1a" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Task/usage-1a>
].
<http://example.org/fhir/DiagnosticReport/report-withGrouping> a fhir:DiagnosticReport;
fhir:Resource.id [ fhir:value "report-withGrouping"];
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report> ]
];
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"report-withGrouping\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-genomics-report.html\">Genomics Report</a></p></div><p><b>basedOn</b>: <a href=\"#ServiceRequest_ExampleServiceRequest\">See above (ServiceRequest/ExampleServiceRequest)</a></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_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>result</b>: </p><ul><li><a href=\"#Observation_overall-interp-1a\">See above (Observation/overall-interp-1a)</a></li><li><a href=\"#Observation_discrete-variant-1a\">See above (Observation/discrete-variant-1a)</a></li><li><a href=\"#Observation_dis-path-1a\">See above (Observation/dis-path-1a)</a></li><li><a href=\"#Observation_complex-variant-1a\">See above (Observation/complex-variant-1a)</a></li><li><a href=\"#Observation_complex-dis-path-1a\">See above (Observation/complex-dis-path-1a)</a></li><li><a href=\"#Observation_pharmPanel-1a\">See above (Observation/pharmPanel-1a)</a></li><li><a href=\"#Observation_haplotype-1a\">See above (Observation/haplotype-1a)</a></li><li><a href=\"#Observation_genotype-1a\">See above (Observation/genotype-1a)</a></li><li><a href=\"#Observation_metab-1a\">See above (Observation/metab-1a)</a></li><li><a href=\"#Observation_efficacy-1a\">See above (Observation/efficacy-1a)</a></li></ul></div>"
];
fhir:DiagnosticReport.basedOn [
fhir:index 0;
fhir:Reference.reference [ fhir:value "ServiceRequest/ExampleServiceRequest" ]
];
fhir:DiagnosticReport.status [ fhir:value "final"];
fhir:DiagnosticReport.category [
fhir:index 0;
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/v2-0074" ];
fhir:Coding.code [ fhir:value "GE" ] ]
];
fhir:DiagnosticReport.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81247-9;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81247-9" ] ]
];
fhir:DiagnosticReport.subject [
fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
];
fhir:DiagnosticReport.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
fhir:DiagnosticReport.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
fhir:DiagnosticReport.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
];
fhir:DiagnosticReport.result [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Observation/overall-interp-1a" ]
], [
fhir:index 1;
fhir:Reference.reference [ fhir:value "Observation/discrete-variant-1a" ]
], [
fhir:index 2;
fhir:Reference.reference [ fhir:value "Observation/dis-path-1a" ]
], [
fhir:index 3;
fhir:Reference.reference [ fhir:value "Observation/complex-variant-1a" ]
], [
fhir:index 4;
fhir:Reference.reference [ fhir:value "Observation/complex-dis-path-1a" ]
], [
fhir:index 5;
fhir:Reference.reference [ fhir:value "Observation/pharmPanel-1a" ]
], [
fhir:index 6;
fhir:Reference.reference [ fhir:value "Observation/haplotype-1a" ]
], [
fhir:index 7;
fhir:Reference.reference [ fhir:value "Observation/genotype-1a" ]
], [
fhir:index 8;
fhir:Reference.reference [ fhir:value "Observation/metab-1a" ]
], [
fhir:index 9;
fhir:Reference.reference [ fhir:value "Observation/efficacy-1a" ]
];
fhir:DiagnosticReport.presentedForm [
fhir:index 0;
fhir:Attachment.contentType [ fhir:value "text/plain" ];
fhir:Attachment.data [ fhir:value "UHV0IHRoZSByZXBvcnQgdGV4dCBoZXJlIC0gbWltZS1lbmNvZGVk"^^xsd:base64Binary ]
].
<http://example.org/fhir/Patient/ExamplePatient> a fhir:Patient;
fhir:Resource.id [ fhir:value "ExamplePatient"];
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "additional" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">This would contain patient identifiers, demographics, etc.</div>"
].
<http://example.org/fhir/Specimen/ExampleSpecimen> a fhir:Specimen;
fhir:Resource.id [ fhir:value "ExampleSpecimen"];
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 \"ExampleSpecimen\" </p></div><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p></div>"
];
fhir:Specimen.subject [
fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
].
<http://example.org/fhir/Organization/ExampleLab> a fhir:Organization;
fhir:Resource.id [ fhir:value "ExampleLab"];
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 \"ExampleLab\" </p></div><p><b>name</b>: Some lab</p></div>"
];
fhir:Organization.name [ fhir:value "Some lab"].
<http://example.org/fhir/ServiceRequest/ExampleServiceRequest> a fhir:ServiceRequest;
fhir:Resource.id [ fhir:value "ExampleServiceRequest"];
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 \"ExampleServiceRequest\" </p></div><p><b>status</b>: active</p><p><b>intent</b>: original-order</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_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>reasonCode</b>: Worried about family planning <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> ()</span></p></div>"
];
fhir:ServiceRequest.status [ fhir:value "active"];
fhir:ServiceRequest.intent [ fhir:value "original-order"];
fhir:ServiceRequest.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:ServiceRequest.subject [
fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
];
fhir:ServiceRequest.reasonCode [
fhir:index 0;
fhir:CodeableConcept.text [ fhir:value "Worried about family planning" ]
].
<http://example.org/fhir/Observation/overall-interp-1a> a fhir:Observation;
fhir:Resource.id [ fhir:value "overall-interp-1a"];
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/overall-interpretation";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/overall-interpretation> ]
];
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 \"overall-interp-1a\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-overall-interpretation.html\">Overall Interpretation</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>: Discrete variation analysis overall interpretation <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51968-6)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>value</b>: Positive <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6576-8; <a href=\"https://browser.ihtsdotools.org/\">SNOMED CT</a>#10828004)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p></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:51968-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "51968-6" ] ]
];
fhir:Observation.subject [
fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
];
fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
];
fhir:Observation.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6576-8;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6576-8" ];
fhir:Coding.display [ fhir:value "Positive" ] ], [
fhir:index 1;
a sct:10828004;
fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
fhir:Coding.code [ fhir:value "10828004" ];
fhir:Coding.display [ fhir:value "Positive" ] ]
];
fhir:Observation.specimen [
fhir:Reference.reference [ fhir:value "Specimen/ExampleSpecimen" ]
].
<http://example.org/fhir/Observation/discrete-variant-1a> a fhir:Observation;
fhir:Resource.id [ fhir:value "discrete-variant-1a"];
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 \"discrete-variant-1a\" </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_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</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>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Discrete genetic variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81252-9)</span></p><p><b>value</b>: NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (clinvar[???]#30880)</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>: ACAD9 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#21497)</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_014049.4 <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_014049.4)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48013-7)</span></p><p><b>value</b>: NG_017064.1 <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>#NG_017064.1)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic DNA change (gHGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81290-9)</span></p><p><b>value</b>: NC_000003.11:g.128625063C>T <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-hgvs.html\">Human Genome Variation Society nomenclature</a>#NC_000003.11:g.128625063C>T)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Discrete genetic variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81252-9)</span></p><p><b>value</b>: rs368949613 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (Genetic Sequence polymorphism database[137]#rs368949613)</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.1249C>T <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (Human Genome Variation Society nomenclature[15.11]#c.1249C>T)</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.Arg417Cys <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (Human Genome Variation Society nomenclature[15.11]#p.Arg417Cys)</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\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6690-7)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change [Type] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48006-1)</span></p><p><b>value</b>: Missense <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6698-0)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: 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>: Genomic allele start-end <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81254-5)</span></p><p><b>value</b>: 31731-31731</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic alt allele [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69551-0)</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Cytogenetic (chromosome) location <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48001-2)</span></p><p><b>value</b>: 3q21 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> ()</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class [Type] <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>: Germline <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6683-2)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic state <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#53034-5)</span></p><p><b>value</b>: Heterozygous <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6706-1)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample variant allelic frequency [NFr] <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>: 47 %<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code % = '%')</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>: 208 1<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic structural variant copy number <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#82155-3)</span></p><p><b>value</b>: 1 1<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Structural variant reported arrCGH [Ratio] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81299-0)</span></p><p><b>value</b>: 0.48</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Structural variant [Length] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81300-6)</span></p><p><b>value</b>: 1396929 1<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Structural variant outer start and end <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81301-4)</span></p><p><b>value</b>: 13200589-15592000</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Structural variant inner start and end <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81302-2)</span></p><p><b>value</b>: 14184616-15581544</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 "Patient/ExamplePatient" ]
];
fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
];
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.specimen [
fhir:Reference.reference [ fhir:value "Specimen/ExampleSpecimen" ]
];
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81252-9;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81252-9" ];
fhir:Coding.display [ fhir:value "Discrete genetic variant" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/clinvar" ];
fhir:Coding.version [ fhir:value "???" ];
fhir:Coding.code [ fhir:value "30880" ];
fhir:Coding.display [ fhir:value "NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys)" ] ] ]
], [
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:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.genenames.org/geneId" ];
fhir:Coding.code [ fhir:value "21497" ];
fhir:Coding.display [ fhir:value "ACAD9" ] ] ]
], [
fhir:index 2;
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: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_014049.4" ] ] ]
], [
fhir:index 3;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48013-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48013-7" ] ] ];
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 "NG_017064.1" ] ] ]
], [
fhir:index 4;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81290-9;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81290-9" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.code [ fhir:value "NC_000003.11:g.128625063C>T" ] ] ]
], [
fhir:index 5;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81252-9;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81252-9" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/projects/SNP" ];
fhir:Coding.version [ fhir:value "137" ];
fhir:Coding.code [ fhir:value "rs368949613" ] ] ]
], [
fhir:index 6;
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:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.version [ fhir:value "15.11" ];
fhir:Coding.code [ fhir:value "c.1249C>T" ] ] ]
], [
fhir:index 7;
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:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.version [ fhir:value "15.11" ];
fhir:Coding.code [ fhir:value "p.Arg417Cys" ] ] ]
], [
fhir:index 8;
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:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6690-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6690-7" ];
fhir:Coding.display [ fhir:value "Substitution" ] ] ]
], [
fhir:index 9;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48006-1;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48006-1" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6698-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6698-0" ];
fhir:Coding.display [ fhir:value "Missense" ] ] ]
], [
fhir:index 10;
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:Observation.component.valueString [ fhir:value "C" ]
], [
fhir:index 11;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81254-5;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81254-5" ] ] ];
fhir:Observation.component.valueRange [
fhir:Range.low [
fhir:Quantity.value [ fhir:value "31731"^^xsd:decimal ] ];
fhir:Range.high [
fhir:Quantity.value [ fhir:value "31731"^^xsd:decimal ] ] ]
], [
fhir:index 12;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:69551-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "69551-0" ] ] ];
fhir:Observation.component.valueString [ fhir:value "T" ]
], [
fhir:index 13;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48001-2;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48001-2" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.text [ fhir:value "3q21" ] ]
], [
fhir:index 14;
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:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6683-2;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6683-2" ];
fhir:Coding.display [ fhir:value "Germline" ] ] ]
], [
fhir:index 15;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:53034-5;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "53034-5" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6706-1;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6706-1" ];
fhir:Coding.display [ fhir:value "Heterozygous" ] ] ]
], [
fhir:index 16;
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:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "47"^^xsd:decimal ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "%" ] ]
], [
fhir:index 17;
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:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "208"^^xsd:decimal ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "1" ] ]
], [
fhir:index 18;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:82155-3;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "82155-3" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "1"^^xsd:decimal ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "1" ] ]
], [
fhir:index 19;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81299-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81299-0" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "0.48"^^xsd:decimal ] ]
], [
fhir:index 20;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81300-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81300-6" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "1396929"^^xsd:decimal ];
fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
fhir:Quantity.code [ fhir:value "1" ] ]
], [
fhir:index 21;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81301-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81301-4" ] ] ];
fhir:Observation.component.valueRange [
fhir:Range.low [
fhir:Quantity.value [ fhir:value "13200589"^^xsd:decimal ] ];
fhir:Range.high [
fhir:Quantity.value [ fhir:value "15592000"^^xsd:decimal ] ] ]
], [
fhir:index 22;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81302-2;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81302-2" ] ] ];
fhir:Observation.component.valueRange [
fhir:Range.low [
fhir:Quantity.value [ fhir:value "14184616"^^xsd:decimal ] ];
fhir:Range.high [
fhir:Quantity.value [ fhir:value "15581544"^^xsd:decimal ] ] ]
].
<http://example.org/fhir/Observation/dis-path-1a> a fhir:Observation;
fhir:Resource.id [ fhir:value "dis-path-1a"];
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication> ]
];
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "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 \"dis-path-1a\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-diagnostic-implication.html\">Diagnostic Implication</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>: Diagnostic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#diagnostic-implication)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_discrete-variant-1a\">See above (Observation/discrete-variant-1a)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Genetic variation clinical significance [Imp] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#53037-8)</span></p><p><b>value</b>: Pathogenic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6668-3)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Associated phenotype <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81259-4)</span></p><p><b>value</b>: Acyl-CoA dehydrogenase family, member 9, deficiency of <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (medgen#C1970173)</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;
fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" ];
fhir:Coding.code [ fhir:value "diagnostic-implication" ] ]
];
fhir:Observation.subject [
fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
];
fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
];
fhir:Observation.derivedFrom [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Observation/discrete-variant-1a" ]
];
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:53037-8;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "53037-8" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6668-3;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6668-3" ];
fhir:Coding.display [ fhir:value "Pathogenic" ] ] ]
], [
fhir:index 1;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81259-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81259-4" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/medgen" ];
fhir:Coding.code [ fhir:value "C1970173" ];
fhir:Coding.display [ fhir:value "Acyl-CoA dehydrogenase family, member 9, deficiency of" ] ] ]
].
<http://example.org/fhir/Observation/complex-variant-1a> a fhir:Observation;
fhir:Resource.id [ fhir:value "complex-variant-1a"];
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 \"complex-variant-1a\" </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_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</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>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><p><b>hasMember</b>: </p><ul><li><a href=\"#Observation_complex-component-D-1a\">See above (Observation/complex-component-D-1a)</a></li><li><a href=\"#Observation_complex-component-E-1a\">See above (Observation/complex-component-E-1a)</a></li></ul><h3>Components</h3><table class=\"grid\"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td>Complex variant type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81263-6)</span></td><td>Haplotype <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA26218-0)</span></td></tr></table></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:Observation.subject [
fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
];
fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
];
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.specimen [
fhir:Reference.reference [ fhir:value "Specimen/ExampleSpecimen" ]
];
fhir:Observation.hasMember [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Observation/complex-component-D-1a" ]
], [
fhir:index 1;
fhir:Reference.reference [ fhir:value "Observation/complex-component-E-1a" ]
];
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81263-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81263-6" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA26218-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA26218-0" ];
fhir:Coding.display [ fhir:value "Haplotype" ] ] ]
].
<http://example.org/fhir/Observation/complex-dis-path-1a> a fhir:Observation;
fhir:Resource.id [ fhir:value "complex-dis-path-1a"];
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication> ]
];
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "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 \"complex-dis-path-1a\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-diagnostic-implication.html\">Diagnostic Implication</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>: Diagnostic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#diagnostic-implication)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_complex-variant-1a\">See above (Observation/complex-variant-1a)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Genetic variation clinical significance [Imp] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#53037-8)</span></p><p><b>value</b>: Pathogenic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6668-3)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Associated phenotype <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81259-4)</span></p><p><b>value</b>: Debrisoquine adverse reaction (disorder) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://browser.ihtsdotools.org/\">SNOMED CT</a>#293498008)</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;
fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" ];
fhir:Coding.code [ fhir:value "diagnostic-implication" ] ]
];
fhir:Observation.subject [
fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
];
fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
];
fhir:Observation.derivedFrom [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Observation/complex-variant-1a" ]
];
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:53037-8;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "53037-8" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6668-3;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6668-3" ];
fhir:Coding.display [ fhir:value "Pathogenic" ] ] ]
], [
fhir:index 1;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81259-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81259-4" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a sct:293498008;
fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
fhir:Coding.code [ fhir:value "293498008" ];
fhir:Coding.display [ fhir:value "Debrisoquine adverse reaction (disorder)" ] ] ]
].
<http://example.org/fhir/Observation/complex-component-D-1a> a fhir:Observation;
fhir:Resource.id [ fhir:value "complex-component-D-1a"];
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 \"complex-component-D-1a\" </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_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</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>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Discrete genetic variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81252-9)</span></p><p><b>value</b>: NM_000106.5(CYP2D6):c.886C>T (p.Arg296Cys) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (clinvar#31934)</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_000106.5 <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_000106.5)</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.886C>T <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (Human Genome Variation Society nomenclature[15.11]#c.886C>T)</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.Arg296Cys <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (Human Genome Variation Society nomenclature[15.11]#p.Arg296Cys)</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\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6690-7)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change [Type] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48006-1)</span></p><p><b>value</b>: Missense <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6698-0)</span></p></blockquote></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 "Patient/ExamplePatient" ]
];
fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
];
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.specimen [
fhir:Reference.reference [ fhir:value "Specimen/ExampleSpecimen" ]
];
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81252-9;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81252-9" ];
fhir:Coding.display [ fhir:value "Discrete genetic variant" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/clinvar" ];
fhir:Coding.code [ fhir:value "31934" ];
fhir:Coding.display [ fhir:value "NM_000106.5(CYP2D6):c.886C>T (p.Arg296Cys)" ] ] ]
], [
fhir:index 1;
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: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_000106.5" ] ] ]
], [
fhir:index 2;
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:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.version [ fhir:value "15.11" ];
fhir:Coding.code [ fhir:value "c.886C>T" ] ] ]
], [
fhir:index 3;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48005-3;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48005-3" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.version [ fhir:value "15.11" ];
fhir:Coding.code [ fhir:value "p.Arg296Cys" ] ] ]
], [
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:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6690-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6690-7" ];
fhir:Coding.display [ fhir:value "Substitution" ] ] ]
], [
fhir:index 5;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48006-1;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48006-1" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6698-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6698-0" ];
fhir:Coding.display [ fhir:value "Missense" ] ] ]
].
<http://example.org/fhir/Observation/complex-component-E-1a> a fhir:Observation;
fhir:Resource.id [ fhir:value "complex-component-E-1a"];
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 \"complex-component-E-1a\" </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_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</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>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Discrete genetic variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81252-9)</span></p><p><b>value</b>: NM_000106.5(CYP2D6):c.1457G>C (p.Ser486Thr) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (clinvar[???]#38486)</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_000106.5 <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_000106.5)</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.1457G>C <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (Human Genome Variation Society nomenclature[15.11]#c.1457G>C)</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 "Patient/ExamplePatient" ]
];
fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
];
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.specimen [
fhir:Reference.reference [ fhir:value "Specimen/ExampleSpecimen" ]
];
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:81252-9;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81252-9" ];
fhir:Coding.display [ fhir:value "Discrete genetic variant" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/clinvar" ];
fhir:Coding.version [ fhir:value "???" ];
fhir:Coding.code [ fhir:value "38486" ];
fhir:Coding.display [ fhir:value "NM_000106.5(CYP2D6):c.1457G>C (p.Ser486Thr)" ] ] ]
], [
fhir:index 1;
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: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_000106.5" ] ] ]
], [
fhir:index 2;
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:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.version [ fhir:value "15.11" ];
fhir:Coding.code [ fhir:value "c.1457G>C" ] ] ]
].
<http://example.org/fhir/Observation/pharmPanel-1a> a fhir:Observation;
fhir:Resource.id [ fhir:value "pharmPanel-1a"];
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "extensions" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"pharmPanel-1a\" </p></div><p><b>Recommended Action</b>: <a href=\"#Task_usage-1a\">See above (Task/usage-1a)</a></p><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>: Panel <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (ncimeta.nci.nih.gov#C43359)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>hasMember</b>: </p><ul><li><a href=\"#Observation_haplotype-1a\">See above (Observation/haplotype-1a)</a></li><li><a href=\"#Observation_genotype-1a\">See above (Observation/genotype-1a)</a></li><li><a href=\"#Observation_metab-1a\">See above (Observation/metab-1a)</a></li><li><a href=\"#Observation_efficacy-1a\">See above (Observation/efficacy-1a)</a></li></ul></div>"
];
fhir:DomainResource.extension [
fhir:index 0;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action" ];
fhir:Extension.valueReference [
fhir:Reference.reference [ fhir:value "Task/usage-1a" ] ]
];
fhir:Observation.status [ fhir:value "final"];
fhir:Observation.category [
fhir:index 0;
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/observation-category" ];
fhir:Coding.code [ fhir:value "laboratory" ] ]
];
fhir:Observation.code [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://ncimeta.nci.nih.gov" ];
fhir:Coding.code [ fhir:value "C43359" ];
fhir:Coding.display [ fhir:value "Panel" ] ]
];
fhir:Observation.subject [
fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
];
fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
];
fhir:Observation.hasMember [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Observation/haplotype-1a" ]
], [
fhir:index 1;
fhir:Reference.reference [ fhir:value "Observation/genotype-1a" ]
], [
fhir:index 2;
fhir:Reference.reference [ fhir:value "Observation/metab-1a" ]
], [
fhir:index 3;
fhir:Reference.reference [ fhir:value "Observation/efficacy-1a" ]
].
<http://example.org/fhir/Observation/haplotype-1a> a fhir:Observation;
fhir:Resource.id [ fhir:value "haplotype-1a"];
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype> ]
];
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 \"haplotype-1a\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-haplotype.html\">Haplotype</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>: Haplotype name <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#84414-2)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>value</b>: *2 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (hla#*2)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_discrete-variant-1a\">See above (Observation/discrete-variant-1a)</a></p></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:84414-2;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "84414-2" ] ]
];
fhir:Observation.subject [
fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
];
fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
];
fhir:Observation.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ebi.ac.uk/ipd/imgt/hla" ];
fhir:Coding.code [ fhir:value "*2" ] ]
];
fhir:Observation.specimen [
fhir:Reference.reference [ fhir:value "Specimen/ExampleSpecimen" ]
];
fhir:Observation.derivedFrom [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Observation/discrete-variant-1a" ]
].
<http://example.org/fhir/Observation/genotype-1a> a fhir:Observation;
fhir:Resource.id [ fhir:value "genotype-1a"];
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype> ]
];
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 \"genotype-1a\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-genotype.html\">Genotype</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>: Genotype display name <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#84413-4)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>value</b>: CYP2C9 *2/*5 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (www.pharmvar.org#CYP2C9 *2/*5)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_haplotype-1a\">See above (Observation/haplotype-1a)</a></p><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>: CYP2C9 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#2623)</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>: VKORC1 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#23663)</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:84413-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "84413-4" ] ]
];
fhir:Observation.subject [
fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
];
fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
];
fhir:Observation.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.pharmvar.org" ];
fhir:Coding.code [ fhir:value "CYP2C9 *2/*5" ];
fhir:Coding.display [ fhir:value "CYP2C9 *2/*5" ] ]
];
fhir:Observation.specimen [
fhir:Reference.reference [ fhir:value "Specimen/ExampleSpecimen" ]
];
fhir:Observation.derivedFrom [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Observation/haplotype-1a" ]
];
fhir:Observation.component [
fhir:index 0;
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:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.genenames.org/geneId" ];
fhir:Coding.code [ fhir:value "2623" ];
fhir:Coding.display [ fhir:value "CYP2C9" ] ] ]
], [
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:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.genenames.org/geneId" ];
fhir:Coding.code [ fhir:value "23663" ];
fhir:Coding.display [ fhir:value "VKORC1" ] ] ]
].
<http://example.org/fhir/Observation/metab-1a> a fhir:Observation;
fhir:Resource.id [ fhir:value "metab-1a"];
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication> ]
];
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 \"metab-1a\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-therapeutic-implication.html\">Therapeutic Implication</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>: Therapeutic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#therapeutic-implication)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_genotype-1a\">See above (Observation/genotype-1a)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Medication assessed [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51963-7)</span></p><p><b>value</b>: Warfarin <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-rxNorm.html\">RxNorm</a>#11289)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Predicted Therapeutic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#predicted-therapeutic-implication)</span></p><p><b>value</b>: Rapid metabolizer <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA25390-8)</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;
fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" ];
fhir:Coding.code [ fhir:value "therapeutic-implication" ] ]
];
fhir:Observation.subject [
fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
];
fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
];
fhir:Observation.derivedFrom [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Observation/genotype-1a" ]
];
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:51963-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "51963-7" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.nlm.nih.gov/research/umls/rxnorm" ];
fhir:Coding.code [ fhir:value "11289" ];
fhir:Coding.display [ fhir:value "Warfarin" ] ] ]
], [
fhir:index 1;
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 "predicted-therapeutic-implication" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA25390-8;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA25390-8" ];
fhir:Coding.display [ fhir:value "Rapid metabolizer" ] ] ]
].
<http://example.org/fhir/Observation/efficacy-1a> a fhir:Observation;
fhir:Resource.id [ fhir:value "efficacy-1a"];
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication> ]
];
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 \"efficacy-1a\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-therapeutic-implication.html\">Therapeutic Implication</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>: Therapeutic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#therapeutic-implication)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_genotype-1a\">See above (Observation/genotype-1a)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Predicted Therapeutic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#predicted-therapeutic-implication)</span></p><p><b>value</b>: Resistant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6676-6)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Medication assessed [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51963-7)</span></p><p><b>value</b>: Warfarin <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-rxNorm.html\">RxNorm</a>#11289)</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;
fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" ];
fhir:Coding.code [ fhir:value "therapeutic-implication" ] ]
];
fhir:Observation.subject [
fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
];
fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
];
fhir:Observation.derivedFrom [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Observation/genotype-1a" ]
];
fhir:Observation.component [
fhir:index 0;
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 "predicted-therapeutic-implication" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6676-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6676-6" ];
fhir:Coding.display [ fhir:value "Resistant" ] ] ]
], [
fhir:index 1;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:51963-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "51963-7" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.nlm.nih.gov/research/umls/rxnorm" ];
fhir:Coding.code [ fhir:value "11289" ];
fhir:Coding.display [ fhir:value "Warfarin" ] ] ]
].
<http://example.org/fhir/Observation/highrisk-1a> a fhir:Observation;
fhir:Resource.id [ fhir:value "highrisk-1a"];
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication> ]
];
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 \"highrisk-1a\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-therapeutic-implication.html\">Therapeutic Implication</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>: Therapeutic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#therapeutic-implication)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_genotype-1a\">See above (Observation/genotype-1a)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Predicted Therapeutic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#predicted-therapeutic-implication)</span></p><p><b>value</b>: Low risk <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA19542-2)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Medication assessed [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51963-7)</span></p><p><b>value</b>: Warfarin <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-rxNorm.html\">RxNorm</a>#11289)</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;
fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" ];
fhir:Coding.code [ fhir:value "therapeutic-implication" ] ]
];
fhir:Observation.subject [
fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
];
fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
];
fhir:Observation.derivedFrom [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Observation/genotype-1a" ]
];
fhir:Observation.component [
fhir:index 0;
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 "predicted-therapeutic-implication" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA19542-2;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA19542-2" ];
fhir:Coding.display [ fhir:value "Low risk" ] ] ]
], [
fhir:index 1;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:51963-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "51963-7" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.nlm.nih.gov/research/umls/rxnorm" ];
fhir:Coding.code [ fhir:value "11289" ];
fhir:Coding.display [ fhir:value "Warfarin" ] ] ]
].
<http://example.org/fhir/Task/usage-1a> a fhir:Task;
fhir:Resource.id [ fhir:value "usage-1a"];
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-recommendation";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-recommendation> ]
];
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 \"usage-1a\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-medication-recommendation.html\">Medication Recommendation</a></p></div><p><b>status</b>: requested</p><p><b>intent</b>: proposal</p><p><b>code</b>: May need higher dosage than usual. <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA26423-6 \"Increase dose\")</span></p><p><b>focus</b>: <a href=\"MedicationStatement-MedicationStatementWarfarin.html\">MedicationStatement/MedicationStatementWarfarin</a></p><p><b>for</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>requester</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>reasonReference</b>: <a href=\"#Observation_metab-1a\">See above (Observation/metab-1a)</a></p></div>"
];
fhir:Task.status [ fhir:value "requested"];
fhir:Task.intent [ fhir:value "proposal"];
fhir:Task.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA26423-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA26423-6" ];
fhir:Coding.display [ fhir:value "Increase dose" ] ];
fhir:CodeableConcept.text [ fhir:value "May need higher dosage than usual." ]
];
fhir:Task.focus [
fhir:Reference.reference [ fhir:value "MedicationStatement/MedicationStatementWarfarin" ]
];
fhir:Task.for [
fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
];
fhir:Task.requester [
fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
];
fhir:Task.reasonReference [
fhir:Reference.reference [ fhir:value "Observation/metab-1a" ]
].
# - 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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