Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions
@prefix fhir: <http://hl7.org/fhir/> . @prefix loinc: <https://loinc.org/rdf/> . @prefix owl: <http://www.w3.org/2002/07/owl#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . # - resource ------------------------------------------------------------------- a fhir:Bundle ; fhir:nodeRole fhir:treeRoot ; fhir:id [ fhir:v "bundle-pgxexample"] ; # fhir:type [ fhir:v "transaction"] ; # fhir:entry ( [ fhir:fullUrl [ fhir:v "http://example.org/fhir/DiagnosticReport/pgx-report"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/DiagnosticReport/pgx-report> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "DiagnosticReport"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Patient/ExamplePatient"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Patient/ExamplePatient> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Patient"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Specimen/ExampleSpecimen"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Specimen/ExampleSpecimen> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Specimen"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Organization/ExampleLab"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Organization/ExampleLab> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Organization"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/ServiceRequest/pgx-request"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/ServiceRequest/pgx-request> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "ServiceRequest"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/med-impact-pgx-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/med-impact-pgx-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Observation"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/genotype-pgx-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/genotype-pgx-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Observation"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/haplotype-1-pgx-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/haplotype-1-pgx-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Observation"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/haplotype-2-pgx-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/haplotype-2-pgx-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Observation"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/variant-1-pgx-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/variant-1-pgx-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Observation"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/variant-2-pgx-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/variant-2-pgx-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Observation"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/MolecularSequence/sequence-1-pgx-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/MolecularSequence/sequence-1-pgx-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "MolecularSequence"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/MolecularSequence/sequence-2-pgx-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/MolecularSequence/sequence-2-pgx-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "MolecularSequence"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Task/med-usage-impact-task-pgx-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Task/med-usage-impact-task-pgx-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Task"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/MedicationStatement/current-med-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/MedicationStatement/current-med-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "MedicationStatement"^^xsd:anyURI ] ] ] ) . # <http://example.org/fhir/DiagnosticReport/pgx-report> a fhir:DiagnosticReport ; fhir:id [ fhir:v "pgx-report"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "extensions" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: DiagnosticReport</b><a name=\"pgx-report\"> </a></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 DiagnosticReport "pgx-report" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-genomic-report.html\">Genomic Report</a></p></div><p><b>Recommended Action</b>: <a href=\"#Task_med-usage-impact-task-pgx-example\">See above (Task/med-usage-impact-task-pgx-example)</a></p><p><b>basedOn</b>: <a href=\"#ServiceRequest_pgx-request\">See above (ServiceRequest/pgx-request)</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/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Genetic analysis report <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51969-4)</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>: Mar 6, 2018, 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_med-impact-pgx-example\">See above (Observation/med-impact-pgx-example: genetics impact for medication metabolism accessment)</a></li><li><a href=\"#Observation_genotype-pgx-example\">See above (Observation/genotype-pgx-example)</a></li><li><a href=\"#Observation_haplotype-1-pgx-example\">See above (Observation/haplotype-1-pgx-example)</a></li><li><a href=\"#Observation_haplotype-2-pgx-example\">See above (Observation/haplotype-2-pgx-example)</a></li><li><a href=\"#Observation_variant-1-pgx-example\">See above (Observation/variant-1-pgx-example)</a></li><li><a href=\"#Observation_variant-2-pgx-example\">See above (Observation/variant-2-pgx-example)</a></li></ul></div>" ] ; # fhir:extension ( [ fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action"^^xsd:anyURI ] ; fhir:value [ a fhir:Reference ; fhir:reference [ fhir:v "Task/med-usage-impact-task-pgx-example" ] ] ] ) ; # fhir:basedOn ( [ fhir:reference [ fhir:v "ServiceRequest/pgx-request" ] ] ) ; # fhir:status [ fhir:v "final"] ; # fhir:category ( [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ; fhir:code [ fhir:v "GE" ] ] ) ] ) ; # fhir:code [ ( fhir:coding [ a loinc:51969-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "51969-4" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:result ( [ fhir:reference [ fhir:v "Observation/med-impact-pgx-example" ] ; fhir:display [ fhir:v "genetics impact for medication metabolism accessment" ] ] [ fhir:reference [ fhir:v "Observation/genotype-pgx-example" ] ] [ fhir:reference [ fhir:v "Observation/haplotype-1-pgx-example" ] ] [ fhir:reference [ fhir:v "Observation/haplotype-2-pgx-example" ] ] [ fhir:reference [ fhir:v "Observation/variant-1-pgx-example" ] ] [ fhir:reference [ fhir:v "Observation/variant-2-pgx-example" ] ] ) . # <http://example.org/fhir/Patient/ExamplePatient> a fhir:Patient ; fhir:id [ fhir:v "ExamplePatient"] ; # fhir:text [ fhir:status [ fhir:v "additional" ] ; fhir: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:id [ fhir:v "ExampleSpecimen"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Specimen</b><a name=\"ExampleSpecimen\"> </a></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 Specimen "ExampleSpecimen" </p></div><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p></div>" ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] . # <http://example.org/fhir/Organization/ExampleLab> a fhir:Organization ; fhir:id [ fhir:v "ExampleLab"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Organization</b><a name=\"ExampleLab\"> </a></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 Organization "ExampleLab" </p></div><p><b>name</b>: Some lab</p></div>" ] ; # fhir:name [ fhir:v "Some lab"] . # <http://example.org/fhir/ServiceRequest/pgx-request> a fhir:ServiceRequest ; fhir:id [ fhir:v "pgx-request"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: ServiceRequest</b><a name=\"pgx-request\"> </a></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 ServiceRequest "pgx-request" </p></div><p><b>status</b>: active</p><p><b>intent</b>: original-order</p><p><b>code</b>: Genetic analysis report <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51969-4)</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:status [ fhir:v "active"] ; # fhir:intent [ fhir:v "original-order"] ; # fhir:code [ ( fhir:coding [ a loinc:51969-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "51969-4" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:reasonCode ( [ fhir:text [ fhir:v "Worried about family planning" ] ] ) . # <http://example.org/fhir/Observation/med-impact-pgx-example> a fhir:Observation ; fhir:id [ fhir:v "med-impact-pgx-example"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Observation</b><a name=\"med-impact-pgx-example\"> </a></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 Observation "med-impact-pgx-example" </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/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</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>: 2018</p><p><b>issued</b>: Mar 6, 2018, 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-pgx-example\">See above (Observation/genotype-pgx-example)</a></p><blockquote><p><b>component</b></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>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><blockquote><p><b>component</b></p><p><b>code</b>: Medication assessed <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>: mercaptopurine <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-rxNorm.html\">RxNorm</a>#103)</span></p></blockquote></div>" ] ; # fhir:status [ fhir:v "final"] ; # fhir:category ( [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ; fhir:code [ fhir:v "laboratory" ] ] ) ] [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ; fhir:code [ fhir:v "GE" ] ] ) ] ) ; # fhir:code [ ( fhir:coding [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ; fhir:code [ fhir:v "therapeutic-implication" ] ; fhir:display [ fhir:v "Therapeutic Implication" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2018"^^xsd:gYear] ; # fhir:issued [ fhir:v "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/genotype-pgx-example" ] ] ) ; # fhir:component ( [ fhir:code [ ( fhir:coding [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ; fhir:code [ fhir:v "therapeutic-implication" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA25390-8 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA25390-8" ] ; fhir:display [ fhir:v "Rapid metabolizer" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:51963-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "51963-7" ] ; fhir:display [ fhir:v "Medication assessed" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.nlm.nih.gov/research/umls/rxnorm"^^xsd:anyURI ] ; fhir:code [ fhir:v "103" ] ; fhir:display [ fhir:v "mercaptopurine" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/genotype-pgx-example> a fhir:Observation ; fhir:id [ fhir:v "genotype-pgx-example"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Observation</b><a name=\"genotype-pgx-example\"> </a></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 Observation "genotype-pgx-example" </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/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</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>: 2018</p><p><b>issued</b>: Mar 6, 2018, 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>value</b>: CYP2C9 *4/*35B <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (www.pharmvar.org#"CYP2C9)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><p><b>derivedFrom</b>: </p><ul><li><a href=\"#Observation_haplotype-1-pgx-example\">See above (Observation/haplotype-1-pgx-example)</a></li><li><a href=\"#Observation_haplotype-2-pgx-example\">See above (Observation/haplotype-2-pgx-example)</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>Gene studied ID <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48018-6)</span></td><td>CYP2C9 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgnc.html\">HUGO Gene Nomenclature Committee Genes</a>#HGNC:2623)</span></td></tr></table></div>" ] ; # fhir:status [ fhir:v "final"] ; # fhir:category ( [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ; fhir:code [ fhir:v "laboratory" ] ] ) ] [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ; fhir:code [ fhir:v "GE" ] ] ) ] ) ; # fhir:code [ ( fhir:coding [ a loinc:84413-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "84413-4" ] ; fhir:display [ fhir:v "genotype display name" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2018"^^xsd:gYear] ; # fhir:issued [ fhir:v "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.pharmvar.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "\"CYP2C9" ] ; fhir:display [ fhir:v "CYP2C9 *4/*35B" ] ] ) ] ; # fhir:specimen [ fhir:reference [ fhir:v "Specimen/ExampleSpecimen" ] ] ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/haplotype-1-pgx-example" ] ] [ fhir:reference [ fhir:v "Observation/haplotype-2-pgx-example" ] ] ) ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:48018-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48018-6" ] ; fhir:display [ fhir:v "Gene studied ID" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "HGNC:2623" ] ; fhir:display [ fhir:v "CYP2C9" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/haplotype-1-pgx-example> a fhir:Observation ; fhir:id [ fhir:v "haplotype-1-pgx-example"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Observation</b><a name=\"haplotype-1-pgx-example\"> </a></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 Observation "haplotype-1-pgx-example" </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/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</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>: 2018</p><p><b>issued</b>: Mar 6, 2018, 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>value</b>: CYP2C9 *35B <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (www.pharmvar.org#"CYP2C9)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_variant-1-pgx-example\">See above (Observation/variant-1-pgx-example)</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>Gene studied ID <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48018-6)</span></td><td>CYP2C9 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgnc.html\">HUGO Gene Nomenclature Committee Genes</a>#HGNC:2623)</span></td></tr></table></div>" ] ; # fhir:status [ fhir:v "final"] ; # fhir:category ( [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ; fhir:code [ fhir:v "laboratory" ] ] ) ] [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ; fhir:code [ fhir:v "GE" ] ] ) ] ) ; # fhir:code [ ( fhir:coding [ a loinc:84414-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "84414-2" ] ; fhir:display [ fhir:v "Haplotype Name" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2018"^^xsd:gYear] ; # fhir:issued [ fhir:v "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.pharmvar.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "\"CYP2C9" ] ; fhir:display [ fhir:v "CYP2C9 *35B" ] ] ) ] ; # fhir:specimen [ fhir:reference [ fhir:v "Specimen/ExampleSpecimen" ] ] ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/variant-1-pgx-example" ] ] ) ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:48018-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48018-6" ] ; fhir:display [ fhir:v "Gene studied ID" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "HGNC:2623" ] ; fhir:display [ fhir:v "CYP2C9" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/haplotype-2-pgx-example> a fhir:Observation ; fhir:id [ fhir:v "haplotype-2-pgx-example"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Observation</b><a name=\"haplotype-2-pgx-example\"> </a></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 Observation "haplotype-2-pgx-example" </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/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</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>: 2018</p><p><b>issued</b>: Mar 6, 2018, 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>value</b>: CYP2C9 *4 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (www.pharmvar.org#"CYP2C9)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_variant-2-pgx-example\">See above (Observation/variant-2-pgx-example)</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>Gene studied ID <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48018-6)</span></td><td>CYP2C9 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgnc.html\">HUGO Gene Nomenclature Committee Genes</a>#HGNC:2623)</span></td></tr></table></div>" ] ; # fhir:status [ fhir:v "final"] ; # fhir:category ( [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ; fhir:code [ fhir:v "laboratory" ] ] ) ] [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ; fhir:code [ fhir:v "GE" ] ] ) ] ) ; # fhir:code [ ( fhir:coding [ a loinc:84414-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "84414-2" ] ; fhir:display [ fhir:v "Haplotype Name" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2018"^^xsd:gYear] ; # fhir:issued [ fhir:v "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.pharmvar.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "\"CYP2C9" ] ; fhir:display [ fhir:v "CYP2C9 *4" ] ] ) ] ; # fhir:specimen [ fhir:reference [ fhir:v "Specimen/ExampleSpecimen" ] ] ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/variant-2-pgx-example" ] ] ) ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:48018-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48018-6" ] ; fhir:display [ fhir:v "Gene studied ID" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "HGNC:2623" ] ; fhir:display [ fhir:v "CYP2C9" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/variant-1-pgx-example> a fhir:Observation ; fhir:id [ fhir:v "variant-1-pgx-example"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Observation</b><a name=\"variant-1-pgx-example\"> </a></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 Observation "variant-1-pgx-example" </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/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</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>: 2018</p><p><b>issued</b>: Mar 6, 2018, 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>derivedFrom</b>: <a href=\"#MolecularSequence_sequence-1-pgx-example\">See above (MolecularSequence/sequence-1-pgx-example)</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\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgnc.html\">HUGO Gene Nomenclature Committee Genes</a>#HGNC:2623)</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>: rs12345 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-dbSNP.html\">Genetic Sequence polymorphism database</a>#rs12345)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Ref nucleotide <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>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Alt allele <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>: G</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>: 55227976-55227977</p></blockquote></div>" ] ; # fhir:status [ fhir:v "final"] ; # fhir:category ( [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ; fhir:code [ fhir:v "laboratory" ] ] ) ] [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ; fhir:code [ fhir:v "GE" ] ] ) ] ) ; # fhir:code [ ( fhir:coding [ a loinc:69548-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "69548-6" ] ; fhir:display [ fhir:v "Genetic variant assessment" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2018"^^xsd:gYear] ; # fhir:issued [ fhir:v "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA9633-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA9633-4" ] ; fhir:display [ fhir:v "Present" ] ] ) ] ; # fhir:specimen [ fhir:reference [ fhir:v "Specimen/ExampleSpecimen" ] ] ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "MolecularSequence/sequence-1-pgx-example" ] ] ) ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:48018-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48018-6" ] ; fhir:display [ fhir:v "Gene studied ID" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "HGNC:2623" ] ; fhir:display [ fhir:v "CYP2C9" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:81252-9 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81252-9" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/projects/SNP"^^xsd:anyURI ] ; fhir:code [ fhir:v "rs12345" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:69547-8 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "69547-8" ] ; fhir:display [ fhir:v "Ref nucleotide" ] ] ) ] ; fhir:value [ fhir:v "T" ] ] [ fhir:code [ ( fhir:coding [ a loinc:69551-0 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "69551-0" ] ; fhir:display [ fhir:v "Alt allele" ] ] ) ] ; fhir:value [ fhir:v "G" ] ] [ fhir:code [ ( fhir:coding [ a loinc:81254-5 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81254-5" ] ] ) ] ; fhir:value [ a fhir:Range ; fhir:low [ fhir:value [ fhir:v "55227976"^^xsd:decimal ] ] ; fhir:high [ fhir:value [ fhir:v "55227977"^^xsd:decimal ] ] ] ] ) . # <http://example.org/fhir/Observation/variant-2-pgx-example> a fhir:Observation ; fhir:id [ fhir:v "variant-2-pgx-example"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Observation</b><a name=\"variant-2-pgx-example\"> </a></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 Observation "variant-2-pgx-example" </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/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</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>: 2018</p><p><b>issued</b>: Mar 6, 2018, 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>derivedFrom</b>: <a href=\"#MolecularSequence_sequence-2-pgx-example\">See above (MolecularSequence/sequence-2-pgx-example)</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\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgnc.html\">HUGO Gene Nomenclature Committee Genes</a>#HGNC:2623)</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_007726.3 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NG_007726.3)</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>: rs233455 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-dbSNP.html\">Genetic Sequence polymorphism database</a>#rs233455)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Ref nucleotide <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>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Alt allele <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>: G</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>: 55227978-55227979</p></blockquote></div>" ] ; # fhir:status [ fhir:v "final"] ; # fhir:category ( [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ; fhir:code [ fhir:v "laboratory" ] ] ) ] [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ; fhir:code [ fhir:v "GE" ] ] ) ] ) ; # fhir:code [ ( fhir:coding [ a loinc:69548-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "69548-6" ] ; fhir:display [ fhir:v "Genetic variant assessment" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2018"^^xsd:gYear] ; # fhir:issued [ fhir:v "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA9633-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA9633-4" ] ; fhir:display [ fhir:v "Present" ] ] ) ] ; # fhir:specimen [ fhir:reference [ fhir:v "Specimen/ExampleSpecimen" ] ] ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "MolecularSequence/sequence-2-pgx-example" ] ] ) ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:48018-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48018-6" ] ; fhir:display [ fhir:v "Gene studied ID" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "HGNC:2623" ] ; fhir:display [ fhir:v "CYP2C9" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48013-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48013-7" ] ; fhir:display [ fhir:v "Genomic reference sequence ID" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ] ; fhir:code [ fhir:v "NG_007726.3" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:81252-9 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81252-9" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/projects/SNP"^^xsd:anyURI ] ; fhir:code [ fhir:v "rs233455" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:69547-8 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "69547-8" ] ; fhir:display [ fhir:v "Ref nucleotide" ] ] ) ] ; fhir:value [ fhir:v "T" ] ] [ fhir:code [ ( fhir:coding [ a loinc:69551-0 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "69551-0" ] ; fhir:display [ fhir:v "Alt allele" ] ] ) ] ; fhir:value [ fhir:v "G" ] ] [ fhir:code [ ( fhir:coding [ a loinc:81254-5 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81254-5" ] ] ) ] ; fhir:value [ a fhir:Range ; fhir:low [ fhir:value [ fhir:v "55227978"^^xsd:decimal ] ] ; fhir:high [ fhir:value [ fhir:v "55227979"^^xsd:decimal ] ] ] ] ) . # <http://example.org/fhir/MolecularSequence/sequence-1-pgx-example> a fhir:MolecularSequence ; fhir:id [ fhir:v "sequence-1-pgx-example"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: MolecularSequence</b><a name=\"sequence-1-pgx-example\"> </a></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 MolecularSequence "sequence-1-pgx-example" </p></div><p><b>type</b>: dna</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</td><td>NG-007726.3 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NG-007726.3)</span></td><td>55227970</td><td>55227980</td></tr></table></div>" ] ; # fhir:type [ fhir:v "dna"] ; # fhir:coordinateSystem [ fhir:v "0"^^xsd:integer] ; # fhir:referenceSeq [ fhir:orientation [ fhir:v "sense" ] ; fhir:referenceSeqId [ ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ] ; fhir:code [ fhir:v "NG-007726.3" ] ] ) ] ; fhir:windowStart [ fhir:v "55227970"^^xsd:integer ] ; fhir:windowEnd [ fhir:v "55227980"^^xsd:integer ] ] . # <http://example.org/fhir/MolecularSequence/sequence-2-pgx-example> a fhir:MolecularSequence ; fhir:id [ fhir:v "sequence-2-pgx-example"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: MolecularSequence</b><a name=\"sequence-2-pgx-example\"> </a></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 MolecularSequence "sequence-2-pgx-example" </p></div><p><b>type</b>: dna</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</td><td>NG-007726.3 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NG-007726.3)</span></td><td>55227970</td><td>55227980</td></tr></table></div>" ] ; # fhir:type [ fhir:v "dna"] ; # fhir:coordinateSystem [ fhir:v "0"^^xsd:integer] ; # fhir:referenceSeq [ fhir:orientation [ fhir:v "sense" ] ; fhir:referenceSeqId [ ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ] ; fhir:code [ fhir:v "NG-007726.3" ] ] ) ] ; fhir:windowStart [ fhir:v "55227970"^^xsd:integer ] ; fhir:windowEnd [ fhir:v "55227980"^^xsd:integer ] ] . # <http://example.org/fhir/Task/med-usage-impact-task-pgx-example> a fhir:Task ; fhir:id [ fhir:v "med-usage-impact-task-pgx-example"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-recommendation"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-recommendation> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Task</b><a name=\"med-usage-impact-task-pgx-example\"> </a></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 Task "med-usage-impact-task-pgx-example" </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>: Any Increase does Recommendation Text from the provider <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>description</b>: Any Increase does Recommendation Text from the provider</p><p><b>focus</b>: <a href=\"#MedicationStatement_current-med-example\">See above (MedicationStatement/current-med-example)</a></p><p><b>for</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>reasonReference</b>: <a href=\"#Observation_med-impact-pgx-example\">See above (Observation/med-impact-pgx-example)</a></p></div>" ] ; # fhir:status [ fhir:v "requested"] ; # fhir:intent [ fhir:v "proposal"] ; # fhir:code [ ( fhir:coding [ a loinc:LA26423-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA26423-6" ] ; fhir:display [ fhir:v "Increase dose" ] ] ) ; fhir:text [ fhir:v "Any Increase does Recommendation Text from the provider" ] ] ; # fhir:description [ fhir:v "Any Increase does Recommendation Text from the provider"] ; # fhir:focus [ fhir:reference [ fhir:v "MedicationStatement/current-med-example" ] ] ; # fhir:for [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:reasonReference [ fhir:reference [ fhir:v "Observation/med-impact-pgx-example" ] ] . # <http://example.org/fhir/MedicationStatement/current-med-example> a fhir:MedicationStatement ; fhir:id [ fhir:v "current-med-example"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: MedicationStatement</b><a name=\"current-med-example\"> </a></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 MedicationStatement "current-med-example" </p></div><p><b>status</b>: unknown</p><p><b>medication</b>: mercaptopurine <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-rxNorm.html\">RxNorm</a>#103)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p></div>" ] ; # fhir:status [ fhir:v "unknown"] ; # fhir:medication [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.nlm.nih.gov/research/umls/rxnorm"^^xsd:anyURI ] ; fhir:code [ fhir:v "103" ] ; fhir:display [ fhir:v "mercaptopurine" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] . #
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0-ballot based on FHIR 4.0.1. Generated 2023-12-18
Links: Table of Contents |
QA Report
| Version History |
|
Propose a change