Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build
Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions
@prefix fhir: <http://hl7.org/fhir/> . @prefix loinc: <http://loinc.org/rdf#> . @prefix owl: <http://www.w3.org/2002/07/owl#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . # - resource ------------------------------------------------------------------- <http://hl7.org/fhir/Bundle/bundle-pgxexample> a fhir:Bundle ; fhir:nodeRole fhir:treeRoot ; fhir:Resource.id [ fhir:value "bundle-pgxexample"] ; fhir:Bundle.type [ fhir:value "transaction"] ; fhir:Bundle.entry [ fhir:index 0 ; fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/DiagnosticReport/pgx-report" ] ; fhir:Bundle.entry.resource <http://example.org/fhir/DiagnosticReport/pgx-report> ; fhir:Bundle.entry.request [ fhir:Bundle.entry.request.method [ fhir:value "POST" ] ; fhir:Bundle.entry.request.url [ fhir:value "DiagnosticReport" ] ] ], [ 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:Bundle.entry.request [ fhir:Bundle.entry.request.method [ fhir:value "POST" ] ; fhir:Bundle.entry.request.url [ fhir:value "Patient" ] ] ], [ 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:Bundle.entry.request [ fhir:Bundle.entry.request.method [ fhir:value "POST" ] ; fhir:Bundle.entry.request.url [ fhir:value "Specimen" ] ] ], [ fhir:index 3 ; fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Organization/ExampleLab" ] ; fhir:Bundle.entry.resource <http://example.org/fhir/Organization/ExampleLab> ; fhir:Bundle.entry.request [ fhir:Bundle.entry.request.method [ fhir:value "POST" ] ; fhir:Bundle.entry.request.url [ fhir:value "Organization" ] ] ], [ fhir:index 4 ; fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/ServiceRequest/pgx-request" ] ; fhir:Bundle.entry.resource <http://example.org/fhir/ServiceRequest/pgx-request> ; fhir:Bundle.entry.request [ fhir:Bundle.entry.request.method [ fhir:value "POST" ] ; fhir:Bundle.entry.request.url [ fhir:value "ServiceRequest" ] ] ], [ fhir:index 5 ; fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/med-impact-pgx-example" ] ; fhir:Bundle.entry.resource <http://example.org/fhir/Observation/med-impact-pgx-example> ; fhir:Bundle.entry.request [ fhir:Bundle.entry.request.method [ fhir:value "POST" ] ; fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ] ], [ fhir:index 6 ; fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/genotype-pgx-example" ] ; fhir:Bundle.entry.resource <http://example.org/fhir/Observation/genotype-pgx-example> ; fhir:Bundle.entry.request [ fhir:Bundle.entry.request.method [ fhir:value "POST" ] ; fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ] ], [ fhir:index 7 ; fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/haplotype-1-pgx-example" ] ; fhir:Bundle.entry.resource <http://example.org/fhir/Observation/haplotype-1-pgx-example> ; fhir:Bundle.entry.request [ fhir:Bundle.entry.request.method [ fhir:value "POST" ] ; fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ] ], [ fhir:index 8 ; fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/haplotype-2-pgx-example" ] ; fhir:Bundle.entry.resource <http://example.org/fhir/Observation/haplotype-2-pgx-example> ; fhir:Bundle.entry.request [ fhir:Bundle.entry.request.method [ fhir:value "POST" ] ; fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ] ], [ fhir:index 9 ; fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/variant-1-pgx-example" ] ; fhir:Bundle.entry.resource <http://example.org/fhir/Observation/variant-1-pgx-example> ; fhir:Bundle.entry.request [ fhir:Bundle.entry.request.method [ fhir:value "POST" ] ; fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ] ], [ fhir:index 10 ; fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/variant-2-pgx-example" ] ; fhir:Bundle.entry.resource <http://example.org/fhir/Observation/variant-2-pgx-example> ; fhir:Bundle.entry.request [ fhir:Bundle.entry.request.method [ fhir:value "POST" ] ; fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ] ], [ fhir:index 11 ; fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/MolecularSequence/sequence-1-pgx-example" ] ; fhir:Bundle.entry.resource <http://example.org/fhir/MolecularSequence/sequence-1-pgx-example> ; fhir:Bundle.entry.request [ fhir:Bundle.entry.request.method [ fhir:value "POST" ] ; fhir:Bundle.entry.request.url [ fhir:value "MolecularSequence" ] ] ], [ fhir:index 12 ; fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/MolecularSequence/sequence-2-pgx-example" ] ; fhir:Bundle.entry.resource <http://example.org/fhir/MolecularSequence/sequence-2-pgx-example> ; fhir:Bundle.entry.request [ fhir:Bundle.entry.request.method [ fhir:value "POST" ] ; fhir:Bundle.entry.request.url [ fhir:value "MolecularSequence" ] ] ], [ fhir:index 13 ; fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Task/med-usage-impact-task-pgx-example" ] ; fhir:Bundle.entry.resource <http://example.org/fhir/Task/med-usage-impact-task-pgx-example> ; fhir:Bundle.entry.request [ fhir:Bundle.entry.request.method [ fhir:value "POST" ] ; fhir:Bundle.entry.request.url [ fhir:value "Task" ] ] ], [ fhir:index 14 ; fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/MedicationStatement/current-med-example" ] ; fhir:Bundle.entry.resource <http://example.org/fhir/MedicationStatement/current-med-example> ; fhir:Bundle.entry.request [ fhir:Bundle.entry.request.method [ fhir:value "POST" ] ; fhir:Bundle.entry.request.url [ fhir:value "MedicationStatement" ] ] ] . <http://example.org/fhir/DiagnosticReport/pgx-report> a fhir:DiagnosticReport ; fhir:Resource.id [ fhir:value "pgx-report"] ; fhir:Resource.meta [ fhir:Meta.profile [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report" ; fhir:index 0 ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report> ] ] ; fhir:DomainResource.text [ fhir:Narrative.status [ fhir:value "generated" ] ; fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"DiagnosticReport_pgx-report\"> </a><p class=\"res-header-id\"><b>Generated Narrative: DiagnosticReport pgx-report</b></p><a name=\"pgx-report\"> </a><a name=\"hcpgx-report\"> </a><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\"/><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-genomic-report.html\">Genomic Report</a></p></div><h2><span title=\"Codes:{http://loinc.org 51969-4}\">Genetic analysis report</span> (<span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span>) </h2><table class=\"grid\"><tr><td>Subject</td><td>Anonymous Patient (no stated gender), DoB Unknown</td></tr><tr><td>Relevant Time</td><td>2016</td></tr><tr><td>Reported</td><td>2018-03-06 00:00:00-0500</td></tr><tr><td>Performer</td><td> <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></td></tr></table><p><b>Report Details</b></p><table class=\"grid\"><tr><td><b>Code</b></td><td><b>Value</b></td><td><b>Flags</b></td><td><b>Relevant Time</b></td></tr><tr><td><a href=\"Bundle-bundle-pgxexample.html#Observation_med-impact-pgx-example\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></a></td><td/><td>Final</td><td>2018</td></tr><tr><td><a href=\"Bundle-bundle-pgxexample.html#Observation_genotype-pgx-example\"><span title=\"Codes:{http://loinc.org 84413-4}\">genotype display name</span></a></td><td><span title=\"Codes:{http://www.pharmvar.org CYP2C9}\">CYP2C9 *4/*35B</span></td><td>Final</td><td>2018</td></tr><tr><td><a href=\"Bundle-bundle-pgxexample.html#Observation_haplotype-1-pgx-example\"><span title=\"Codes:{http://loinc.org 84414-2}\">Haplotype Name</span></a></td><td><span title=\"Codes:{http://www.pharmvar.org CYP2C9}\">CYP2C9 *35B</span></td><td>Final</td><td>2018</td></tr><tr><td><a href=\"Bundle-bundle-pgxexample.html#Observation_haplotype-2-pgx-example\"><span title=\"Codes:{http://loinc.org 84414-2}\">Haplotype Name</span></a></td><td><span title=\"Codes:{http://www.pharmvar.org CYP2C9}\">CYP2C9 *4</span></td><td>Final</td><td>2018</td></tr><tr><td><a href=\"Bundle-bundle-pgxexample.html#Observation_variant-1-pgx-example\"><span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></a></td><td><span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></td><td>Final</td><td>2018</td></tr><tr><td><a href=\"Bundle-bundle-pgxexample.html#Observation_variant-2-pgx-example\"><span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></a></td><td><span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></td><td>Final</td><td>2018</td></tr></table></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:link <http://hl7.org/fhir/Task/med-usage-impact-task-pgx-example> ; fhir:Reference.reference [ fhir:value "Task/med-usage-impact-task-pgx-example" ] ] ] ; fhir:DiagnosticReport.basedOn [ fhir:index 0 ; fhir:link <http://hl7.org/fhir/ServiceRequest/pgx-request> ; fhir:Reference.reference [ fhir:value "ServiceRequest/pgx-request" ] ] ; 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:51969-4 ; fhir:Coding.system [ fhir:value "http://loinc.org" ] ; fhir:Coding.code [ fhir:value "51969-4" ] ] ] ; fhir:DiagnosticReport.subject [ fhir:link <http://hl7.org/fhir/Patient/ExamplePatient> ; fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ] ] ; fhir:DiagnosticReport.effectiveDateTime [ fhir:value "2016"^^xsd:gYear] ; fhir:DiagnosticReport.issued [ fhir:value "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; fhir:DiagnosticReport.performer [ fhir:index 0 ; fhir:link <http://hl7.org/fhir/Organization/ExampleLab> ; fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ] ] ; fhir:DiagnosticReport.result [ fhir:index 0 ; fhir:link <http://hl7.org/fhir/Observation/med-impact-pgx-example> ; fhir:Reference.reference [ fhir:value "Observation/med-impact-pgx-example" ] ; fhir:Reference.display [ fhir:value "genetics impact for medication metabolism accessment" ] ], [ fhir:index 1 ; fhir:link <http://hl7.org/fhir/Observation/genotype-pgx-example> ; fhir:Reference.reference [ fhir:value "Observation/genotype-pgx-example" ] ], [ fhir:index 2 ; fhir:link <http://hl7.org/fhir/Observation/haplotype-1-pgx-example> ; fhir:Reference.reference [ fhir:value "Observation/haplotype-1-pgx-example" ] ], [ fhir:index 3 ; fhir:link <http://hl7.org/fhir/Observation/haplotype-2-pgx-example> ; fhir:Reference.reference [ fhir:value "Observation/haplotype-2-pgx-example" ] ], [ fhir:index 4 ; fhir:link <http://hl7.org/fhir/Observation/variant-1-pgx-example> ; fhir:Reference.reference [ fhir:value "Observation/variant-1-pgx-example" ] ], [ fhir:index 5 ; fhir:link <http://hl7.org/fhir/Observation/variant-2-pgx-example> ; fhir:Reference.reference [ fhir:value "Observation/variant-2-pgx-example" ] ] . <http://hl7.org/fhir/Task/med-usage-impact-task-pgx-example> a fhir:Task . <http://hl7.org/fhir/ServiceRequest/pgx-request> a fhir:ServiceRequest . <http://hl7.org/fhir/Patient/ExamplePatient> a fhir:Patient . <http://hl7.org/fhir/Organization/ExampleLab> a fhir:Organization . <http://hl7.org/fhir/Observation/med-impact-pgx-example> a fhir:Observation . <http://hl7.org/fhir/Observation/genotype-pgx-example> a fhir:Observation . <http://hl7.org/fhir/Observation/haplotype-1-pgx-example> a fhir:Observation . <http://hl7.org/fhir/Observation/haplotype-2-pgx-example> a fhir:Observation . <http://hl7.org/fhir/Observation/variant-1-pgx-example> a fhir:Observation . <http://hl7.org/fhir/Observation/variant-2-pgx-example> a fhir:Observation . <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\"><a name=\"Patient_ExamplePatient\"> </a>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\"><a name=\"Specimen_ExampleSpecimen\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Specimen ExampleSpecimen</b></p><a name=\"ExampleSpecimen\"> </a><a name=\"hcExampleSpecimen\"> </a><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p></div>" ] ; fhir:Specimen.subject [ fhir:link <http://hl7.org/fhir/Patient/ExamplePatient> ; 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\"><a name=\"Organization_ExampleLab\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Organization ExampleLab</b></p><a name=\"ExampleLab\"> </a><a name=\"hcExampleLab\"> </a><p><b>name</b>: Some lab</p></div>" ] ; fhir:Organization.name [ fhir:value "Some lab"] . <http://example.org/fhir/ServiceRequest/pgx-request> a fhir:ServiceRequest ; fhir:Resource.id [ fhir:value "pgx-request"] ; fhir:DomainResource.text [ fhir:Narrative.status [ fhir:value "generated" ] ; fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"ServiceRequest_pgx-request\"> </a><p class=\"res-header-id\"><b>Generated Narrative: ServiceRequest pgx-request</b></p><a name=\"pgx-request\"> </a><a name=\"hcpgx-request\"> </a><p><b>status</b>: Active</p><p><b>intent</b>: Original Order</p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51969-4}\">Genetic analysis report</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>reasonCode</b>: <span title=\"Codes:\">Worried about family planning</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:51969-4 ; fhir:Coding.system [ fhir:value "http://loinc.org" ] ; fhir:Coding.code [ fhir:value "51969-4" ] ] ] ; fhir:ServiceRequest.subject [ fhir:link <http://hl7.org/fhir/Patient/ExamplePatient> ; 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/med-impact-pgx-example> a fhir:Observation ; fhir:Resource.id [ fhir:value "med-impact-pgx-example"] ; 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\"><a name=\"Observation_med-impact-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation med-impact-pgx-example</b></p><a name=\"med-impact-pgx-example\"> </a><a name=\"hcmed-impact-pgx-example\"> </a><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\"/><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>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-pgxexample.html#Observation_genotype-pgx-example\">Observation genotype display name</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA25390-8}\">Rapid metabolizer</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51963-7}\">Medication assessed</span></p><p><b>value</b>: <span title=\"Codes:{http://www.nlm.nih.gov/research/umls/rxnorm 103}\">mercaptopurine</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:index 1 ; 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: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:Coding.display [ fhir:value "Therapeutic Implication" ] ] ] ; fhir:Observation.subject [ fhir:link <http://hl7.org/fhir/Patient/ExamplePatient> ; fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ] ] ; fhir:Observation.effectiveDateTime [ fhir:value "2018"^^xsd:gYear] ; fhir:Observation.issued [ fhir:value "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; fhir:Observation.performer [ fhir:index 0 ; fhir:link <http://hl7.org/fhir/Organization/ExampleLab> ; fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ] ] ; fhir:Observation.derivedFrom [ fhir:index 0 ; fhir:link <http://hl7.org/fhir/Observation/genotype-pgx-example> ; fhir:Reference.reference [ fhir:value "Observation/genotype-pgx-example" ] ] ; 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 "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" ] ] ] ], [ 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:Coding.display [ fhir:value "Medication assessed" ] ] ] ; 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 "103" ] ; fhir:Coding.display [ fhir:value "mercaptopurine" ] ] ] ] . <http://example.org/fhir/Observation/genotype-pgx-example> a fhir:Observation ; fhir:Resource.id [ fhir:value "genotype-pgx-example"] ; 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\"><a name=\"Observation_genotype-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation genotype-pgx-example</b></p><a name=\"genotype-pgx-example\"> </a><a name=\"hcgenotype-pgx-example\"> </a><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\"/><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>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 84413-4}\">genotype display name</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://www.pharmvar.org CYP2C9}\">CYP2C9 *4/*35B</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>derivedFrom</b>: </p><ul><li><a href=\"Bundle-bundle-pgxexample.html#Observation_haplotype-1-pgx-example\">Observation Haplotype Name</a></li><li><a href=\"Bundle-bundle-pgxexample.html#Observation_haplotype-2-pgx-example\">Observation Haplotype Name</a></li></ul><h3>Components</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://loinc.org 48018-6}\">Gene studied ID</span></td><td><span title=\"Codes:{http://www.genenames.org HGNC:2623}\">CYP2C9</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:index 1 ; 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: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:Coding.display [ fhir:value "genotype display name" ] ] ] ; fhir:Observation.subject [ fhir:link <http://hl7.org/fhir/Patient/ExamplePatient> ; fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ] ] ; fhir:Observation.effectiveDateTime [ fhir:value "2018"^^xsd:gYear] ; fhir:Observation.issued [ fhir:value "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; fhir:Observation.performer [ fhir:index 0 ; fhir:link <http://hl7.org/fhir/Organization/ExampleLab> ; 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" ] ; fhir:Coding.display [ fhir:value "CYP2C9 *4/*35B" ] ] ] ; fhir:Observation.specimen [ fhir:link <http://hl7.org/fhir/Specimen/ExampleSpecimen> ; fhir:Reference.reference [ fhir:value "Specimen/ExampleSpecimen" ] ] ; fhir:Observation.derivedFrom [ fhir:index 0 ; fhir:link <http://hl7.org/fhir/Observation/haplotype-1-pgx-example> ; fhir:Reference.reference [ fhir:value "Observation/haplotype-1-pgx-example" ] ], [ fhir:index 1 ; fhir:link <http://hl7.org/fhir/Observation/haplotype-2-pgx-example> ; fhir:Reference.reference [ fhir:value "Observation/haplotype-2-pgx-example" ] ] ; 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:Coding.display [ fhir:value "Gene studied ID" ] ] ] ; fhir:Observation.component.valueCodeableConcept [ fhir:CodeableConcept.coding [ fhir:index 0 ; fhir:Coding.system [ fhir:value "http://www.genenames.org" ] ; fhir:Coding.code [ fhir:value "HGNC:2623" ] ; fhir:Coding.display [ fhir:value "CYP2C9" ] ] ] ] . <http://hl7.org/fhir/Specimen/ExampleSpecimen> a fhir:Specimen . <http://example.org/fhir/Observation/haplotype-1-pgx-example> a fhir:Observation ; fhir:Resource.id [ fhir:value "haplotype-1-pgx-example"] ; 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\"><a name=\"Observation_haplotype-1-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation haplotype-1-pgx-example</b></p><a name=\"haplotype-1-pgx-example\"> </a><a name=\"hchaplotype-1-pgx-example\"> </a><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\"/><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>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 84414-2}\">Haplotype Name</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://www.pharmvar.org CYP2C9}\">CYP2C9 *35B</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-pgxexample.html#Observation_variant-1-pgx-example\">Observation Genetic variant assessment</a></p><h3>Components</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://loinc.org 48018-6}\">Gene studied ID</span></td><td><span title=\"Codes:{http://www.genenames.org HGNC:2623}\">CYP2C9</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:index 1 ; 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: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:Coding.display [ fhir:value "Haplotype Name" ] ] ] ; fhir:Observation.subject [ fhir:link <http://hl7.org/fhir/Patient/ExamplePatient> ; fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ] ] ; fhir:Observation.effectiveDateTime [ fhir:value "2018"^^xsd:gYear] ; fhir:Observation.issued [ fhir:value "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; fhir:Observation.performer [ fhir:index 0 ; fhir:link <http://hl7.org/fhir/Organization/ExampleLab> ; 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" ] ; fhir:Coding.display [ fhir:value "CYP2C9 *35B" ] ] ] ; fhir:Observation.specimen [ fhir:link <http://hl7.org/fhir/Specimen/ExampleSpecimen> ; fhir:Reference.reference [ fhir:value "Specimen/ExampleSpecimen" ] ] ; fhir:Observation.derivedFrom [ fhir:index 0 ; fhir:link <http://hl7.org/fhir/Observation/variant-1-pgx-example> ; fhir:Reference.reference [ fhir:value "Observation/variant-1-pgx-example" ] ] ; 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:Coding.display [ fhir:value "Gene studied ID" ] ] ] ; fhir:Observation.component.valueCodeableConcept [ fhir:CodeableConcept.coding [ fhir:index 0 ; fhir:Coding.system [ fhir:value "http://www.genenames.org" ] ; fhir:Coding.code [ fhir:value "HGNC:2623" ] ; fhir:Coding.display [ fhir:value "CYP2C9" ] ] ] ] . <http://example.org/fhir/Observation/haplotype-2-pgx-example> a fhir:Observation ; fhir:Resource.id [ fhir:value "haplotype-2-pgx-example"] ; 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\"><a name=\"Observation_haplotype-2-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation haplotype-2-pgx-example</b></p><a name=\"haplotype-2-pgx-example\"> </a><a name=\"hchaplotype-2-pgx-example\"> </a><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\"/><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>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 84414-2}\">Haplotype Name</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://www.pharmvar.org CYP2C9}\">CYP2C9 *4</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-pgxexample.html#Observation_variant-2-pgx-example\">Observation Genetic variant assessment</a></p><h3>Components</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://loinc.org 48018-6}\">Gene studied ID</span></td><td><span title=\"Codes:{http://www.genenames.org HGNC:2623}\">CYP2C9</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:index 1 ; 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: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:Coding.display [ fhir:value "Haplotype Name" ] ] ] ; fhir:Observation.subject [ fhir:link <http://hl7.org/fhir/Patient/ExamplePatient> ; fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ] ] ; fhir:Observation.effectiveDateTime [ fhir:value "2018"^^xsd:gYear] ; fhir:Observation.issued [ fhir:value "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; fhir:Observation.performer [ fhir:index 0 ; fhir:link <http://hl7.org/fhir/Organization/ExampleLab> ; 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" ] ; fhir:Coding.display [ fhir:value "CYP2C9 *4" ] ] ] ; fhir:Observation.specimen [ fhir:link <http://hl7.org/fhir/Specimen/ExampleSpecimen> ; fhir:Reference.reference [ fhir:value "Specimen/ExampleSpecimen" ] ] ; fhir:Observation.derivedFrom [ fhir:index 0 ; fhir:link <http://hl7.org/fhir/Observation/variant-2-pgx-example> ; fhir:Reference.reference [ fhir:value "Observation/variant-2-pgx-example" ] ] ; 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:Coding.display [ fhir:value "Gene studied ID" ] ] ] ; fhir:Observation.component.valueCodeableConcept [ fhir:CodeableConcept.coding [ fhir:index 0 ; fhir:Coding.system [ fhir:value "http://www.genenames.org" ] ; fhir:Coding.code [ fhir:value "HGNC:2623" ] ; fhir:Coding.display [ fhir:value "CYP2C9" ] ] ] ] . <http://example.org/fhir/Observation/variant-1-pgx-example> a fhir:Observation ; fhir:Resource.id [ fhir:value "variant-1-pgx-example"] ; 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\"><a name=\"Observation_variant-1-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation variant-1-pgx-example</b></p><a name=\"variant-1-pgx-example\"> </a><a name=\"hcvariant-1-pgx-example\"> </a><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\"/><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>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-pgxexample.html#MolecularSequence_sequence-1-pgx-example\">MolecularSequence: type = dna; coordinateSystem = 0</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48018-6}\">Gene studied ID</span></p><p><b>value</b>: <span title=\"Codes:{http://www.genenames.org HGNC:2623}\">CYP2C9</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81252-9}\">Discrete genetic variant</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/projects/SNP rs12345}\">rs12345</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69547-8}\">Ref nucleotide</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69551-0}\">Alt allele</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81254-5}\">Genomic allele start-end</span></p><p><b>value</b>: 55227976-55227977</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:index 1 ; 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: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:link <http://hl7.org/fhir/Patient/ExamplePatient> ; fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ] ] ; fhir:Observation.effectiveDateTime [ fhir:value "2018"^^xsd:gYear] ; fhir:Observation.issued [ fhir:value "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; fhir:Observation.performer [ fhir:index 0 ; fhir:link <http://hl7.org/fhir/Organization/ExampleLab> ; 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:link <http://hl7.org/fhir/Specimen/ExampleSpecimen> ; fhir:Reference.reference [ fhir:value "Specimen/ExampleSpecimen" ] ] ; fhir:Observation.derivedFrom [ fhir:index 0 ; fhir:link <http://hl7.org/fhir/MolecularSequence/sequence-1-pgx-example> ; fhir:Reference.reference [ fhir:value "MolecularSequence/sequence-1-pgx-example" ] ] ; 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:Coding.display [ fhir:value "Gene studied ID" ] ] ] ; fhir:Observation.component.valueCodeableConcept [ fhir:CodeableConcept.coding [ fhir:index 0 ; fhir:Coding.system [ fhir:value "http://www.genenames.org" ] ; fhir:Coding.code [ fhir:value "HGNC:2623" ] ; fhir:Coding.display [ fhir:value "CYP2C9" ] ] ] ], [ fhir:index 1 ; 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.code [ fhir:value "rs12345" ] ] ] ], [ fhir:index 2 ; fhir:Observation.component.code [ fhir:CodeableConcept.coding [ fhir:index 0 ; a loinc:69547-8 ; fhir:Coding.system [ fhir:value "http://loinc.org" ] ; fhir:Coding.code [ fhir:value "69547-8" ] ; fhir:Coding.display [ fhir:value "Ref nucleotide" ] ] ] ; fhir:Observation.component.valueString [ fhir:value "T" ] ], [ fhir:index 3 ; 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:Coding.display [ fhir:value "Alt allele" ] ] ] ; fhir:Observation.component.valueString [ fhir:value "G" ] ], [ fhir:index 4 ; 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 "55227976"^^xsd:decimal ] ] ; fhir:Range.high [ fhir:Quantity.value [ fhir:value "55227977"^^xsd:decimal ] ] ] ] . <http://hl7.org/fhir/MolecularSequence/sequence-1-pgx-example> a fhir:MolecularSequence . <http://example.org/fhir/Observation/variant-2-pgx-example> a fhir:Observation ; fhir:Resource.id [ fhir:value "variant-2-pgx-example"] ; 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\"><a name=\"Observation_variant-2-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation variant-2-pgx-example</b></p><a name=\"variant-2-pgx-example\"> </a><a name=\"hcvariant-2-pgx-example\"> </a><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\"/><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>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-pgxexample.html#MolecularSequence_sequence-2-pgx-example\">MolecularSequence: type = dna; coordinateSystem = 0</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48018-6}\">Gene studied ID</span></p><p><b>value</b>: <span title=\"Codes:{http://www.genenames.org HGNC:2623}\">CYP2C9</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48013-7}\">Genomic reference sequence ID</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NG_007726.3}\">NG_007726.3</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81252-9}\">Discrete genetic variant</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/projects/SNP rs233455}\">rs233455</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69547-8}\">Ref nucleotide</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69551-0}\">Alt allele</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81254-5}\">Genomic allele start-end</span></p><p><b>value</b>: 55227978-55227979</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:index 1 ; 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: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:link <http://hl7.org/fhir/Patient/ExamplePatient> ; fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ] ] ; fhir:Observation.effectiveDateTime [ fhir:value "2018"^^xsd:gYear] ; fhir:Observation.issued [ fhir:value "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; fhir:Observation.performer [ fhir:index 0 ; fhir:link <http://hl7.org/fhir/Organization/ExampleLab> ; 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:link <http://hl7.org/fhir/Specimen/ExampleSpecimen> ; fhir:Reference.reference [ fhir:value "Specimen/ExampleSpecimen" ] ] ; fhir:Observation.derivedFrom [ fhir:index 0 ; fhir:link <http://hl7.org/fhir/MolecularSequence/sequence-2-pgx-example> ; fhir:Reference.reference [ fhir:value "MolecularSequence/sequence-2-pgx-example" ] ] ; 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:Coding.display [ fhir:value "Gene studied ID" ] ] ] ; fhir:Observation.component.valueCodeableConcept [ fhir:CodeableConcept.coding [ fhir:index 0 ; fhir:Coding.system [ fhir:value "http://www.genenames.org" ] ; fhir:Coding.code [ fhir:value "HGNC:2623" ] ; fhir:Coding.display [ fhir:value "CYP2C9" ] ] ] ], [ fhir:index 1 ; 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:Coding.display [ fhir:value "Genomic reference sequence ID" ] ] ] ; fhir:Observation.component.valueCodeableConcept [ fhir:CodeableConcept.coding [ fhir:index 0 ; fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ] ; fhir:Coding.code [ fhir:value "NG_007726.3" ] ] ] ], [ fhir:index 2 ; fhir:Observation.component.code [ fhir:CodeableConcept.coding [ fhir:index 0 ; a loinc:81252-9 ; fhir:Coding.system [ fhir:value "http://loinc.org" ] ; fhir:Coding.code [ fhir:value "81252-9" ] ] ] ; fhir:Observation.component.valueCodeableConcept [ fhir:CodeableConcept.coding [ fhir:index 0 ; fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/projects/SNP" ] ; fhir:Coding.code [ fhir:value "rs233455" ] ] ] ], [ fhir:index 3 ; fhir:Observation.component.code [ fhir:CodeableConcept.coding [ fhir:index 0 ; a loinc:69547-8 ; fhir:Coding.system [ fhir:value "http://loinc.org" ] ; fhir:Coding.code [ fhir:value "69547-8" ] ; fhir:Coding.display [ fhir:value "Ref nucleotide" ] ] ] ; fhir:Observation.component.valueString [ fhir:value "T" ] ], [ fhir:index 4 ; 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:Coding.display [ fhir:value "Alt allele" ] ] ] ; fhir:Observation.component.valueString [ fhir:value "G" ] ], [ fhir:index 5 ; 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 "55227978"^^xsd:decimal ] ] ; fhir:Range.high [ fhir:Quantity.value [ fhir:value "55227979"^^xsd:decimal ] ] ] ] . <http://hl7.org/fhir/MolecularSequence/sequence-2-pgx-example> a fhir:MolecularSequence . <http://example.org/fhir/MolecularSequence/sequence-1-pgx-example> a fhir:MolecularSequence ; fhir:Resource.id [ fhir:value "sequence-1-pgx-example"] ; fhir:DomainResource.text [ fhir:Narrative.status [ fhir:value "generated" ] ; fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"MolecularSequence_sequence-1-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: MolecularSequence sequence-1-pgx-example</b></p><a name=\"sequence-1-pgx-example\"> </a><a name=\"hcsequence-1-pgx-example\"> </a><p><b>type</b>: DNA Sequence</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td style=\"display: none\">*</td><td>Sense orientation of referenceSeq</td><td><span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NG-007726.3}\">NG-007726.3</span></td><td>55227970</td><td>55227980</td></tr></table></div>" ] ; fhir:MolecularSequence.type [ fhir:value "dna"] ; fhir:MolecularSequence.coordinateSystem [ fhir:value "0"^^xsd:integer] ; fhir:MolecularSequence.referenceSeq [ fhir:MolecularSequence.referenceSeq.orientation [ fhir:value "sense" ] ; fhir:MolecularSequence.referenceSeq.referenceSeqId [ fhir:CodeableConcept.coding [ fhir:index 0 ; fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ] ; fhir:Coding.code [ fhir:value "NG-007726.3" ] ] ] ; fhir:MolecularSequence.referenceSeq.windowStart [ fhir:value "55227970"^^xsd:integer ] ; fhir:MolecularSequence.referenceSeq.windowEnd [ fhir:value "55227980"^^xsd:integer ] ] . <http://example.org/fhir/MolecularSequence/sequence-2-pgx-example> a fhir:MolecularSequence ; fhir:Resource.id [ fhir:value "sequence-2-pgx-example"] ; fhir:DomainResource.text [ fhir:Narrative.status [ fhir:value "generated" ] ; fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"MolecularSequence_sequence-2-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: MolecularSequence sequence-2-pgx-example</b></p><a name=\"sequence-2-pgx-example\"> </a><a name=\"hcsequence-2-pgx-example\"> </a><p><b>type</b>: DNA Sequence</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td style=\"display: none\">*</td><td>Sense orientation of referenceSeq</td><td><span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NG-007726.3}\">NG-007726.3</span></td><td>55227970</td><td>55227980</td></tr></table></div>" ] ; fhir:MolecularSequence.type [ fhir:value "dna"] ; fhir:MolecularSequence.coordinateSystem [ fhir:value "0"^^xsd:integer] ; fhir:MolecularSequence.referenceSeq [ fhir:MolecularSequence.referenceSeq.orientation [ fhir:value "sense" ] ; fhir:MolecularSequence.referenceSeq.referenceSeqId [ fhir:CodeableConcept.coding [ fhir:index 0 ; fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ] ; fhir:Coding.code [ fhir:value "NG-007726.3" ] ] ] ; fhir:MolecularSequence.referenceSeq.windowStart [ fhir:value "55227970"^^xsd:integer ] ; fhir:MolecularSequence.referenceSeq.windowEnd [ fhir:value "55227980"^^xsd:integer ] ] . <http://example.org/fhir/Task/med-usage-impact-task-pgx-example> a fhir:Task ; fhir:Resource.id [ fhir:value "med-usage-impact-task-pgx-example"] ; 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\"><a name=\"Task_med-usage-impact-task-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Task med-usage-impact-task-pgx-example</b></p><a name=\"med-usage-impact-task-pgx-example\"> </a><a name=\"hcmed-usage-impact-task-pgx-example\"> </a><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\"/><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>: <span title=\"Codes:{http://loinc.org LA26423-6}\">Any Increase does Recommendation Text from the provider</span></p><p><b>description</b>: Any Increase does Recommendation Text from the provider</p><p><b>focus</b>: <a href=\"Bundle-bundle-pgxexample.html#MedicationStatement_current-med-example\">MedicationStatement: status = unknown; medication[x] = mercaptopurine</a></p><p><b>for</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>reasonReference</b>: <a href=\"Bundle-bundle-pgxexample.html#Observation_med-impact-pgx-example\">Observation Therapeutic Implication</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 "Any Increase does Recommendation Text from the provider" ] ] ; fhir:Task.description [ fhir:value "Any Increase does Recommendation Text from the provider"] ; fhir:Task.focus [ fhir:link <http://hl7.org/fhir/MedicationStatement/current-med-example> ; fhir:Reference.reference [ fhir:value "MedicationStatement/current-med-example" ] ] ; fhir:Task.for [ fhir:link <http://hl7.org/fhir/Patient/ExamplePatient> ; fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ] ] ; fhir:Task.reasonReference [ fhir:link <http://hl7.org/fhir/Observation/med-impact-pgx-example> ; fhir:Reference.reference [ fhir:value "Observation/med-impact-pgx-example" ] ] . <http://hl7.org/fhir/MedicationStatement/current-med-example> a fhir:MedicationStatement . <http://example.org/fhir/MedicationStatement/current-med-example> a fhir:MedicationStatement ; fhir:Resource.id [ fhir:value "current-med-example"] ; fhir:DomainResource.text [ fhir:Narrative.status [ fhir:value "generated" ] ; fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"MedicationStatement_current-med-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: MedicationStatement current-med-example</b></p><a name=\"current-med-example\"> </a><a name=\"hccurrent-med-example\"> </a><p><b>status</b>: Unknown</p><p><b>medication</b>: <span title=\"Codes:{http://www.nlm.nih.gov/research/umls/rxnorm 103}\">mercaptopurine</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p></div>" ] ; fhir:MedicationStatement.status [ fhir:value "unknown"] ; fhir:MedicationStatement.medicationCodeableConcept [ fhir:CodeableConcept.coding [ fhir:index 0 ; fhir:Coding.system [ fhir:value "http://www.nlm.nih.gov/research/umls/rxnorm" ] ; fhir:Coding.code [ fhir:value "103" ] ; fhir:Coding.display [ fhir:value "mercaptopurine" ] ] ] ; fhir:MedicationStatement.subject [ fhir:link <http://hl7.org/fhir/Patient/ExamplePatient> ; fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ] ] . # - ontology header ------------------------------------------------------------ <http://hl7.org/fhir/Bundle/bundle-pgxexample.ttl> a owl:Ontology ; owl:imports fhir:fhir.ttl ; owl:versionIRI <http://build.fhir.org/Bundle/bundle-pgxexample.ttl> .
IG © 2025+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#4.0.0-cibuild based on FHIR 4.0.1. Generated 2026-09-21
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