@prefix fhir: . @prefix loinc: . @prefix owl: . @prefix rdf: . @prefix rdfs: . @prefix sct: . @prefix xsd: . # - resource ------------------------------------------------------------------- a fhir:GenomicStudy ; fhir:resourceDefinition http://hl7.org/fhir/StructureDefinition/GenomicStudy|0.1.0-ci-build ; fhir:nodeRole fhir:treeRoot ; fhir:id [ fhir:v "example-pgx"] ; # fhir:language [ fhir:v "en"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div [ fhir:v "

Generated Narrative: GenomicStudy example-pgx

Language: en

identifier: http://example.org/identifiers/genomicstudies/urn:uuid:pgx-study-0001 (use: temp, )

status: Available

type: Molecular genetic test (procedure)

subject: Adam B. Everyman (official) Male, DoB: 1951-01-20 ( Medical record number: m123 (use: usual, period: 2021-01-01 --> (ongoing)))

startDate: 2021-01-01

basedOn: ServiceRequest

interpreter: Practitioner Jane Doel

Reasons

-Concept
*Treatment completed (situation)

note:

PGX panel ordered prior to initiating warfarin therapy to guide dosing based on CYP2C9 and VKORC1 genotype.

\n

description:

Pharmacogenomics sequencing panel targeting protein-coding and exon-splicing regions of CYP2C19, CYP2C9, and VKORC1 to inform drug selection and dosing.

\n

analysis

identifier: http://example.org/identifiers/genomicAnalyses/urn:uuid:pgx-analysis-0001 (use: temp, )

methodType: Sequence analysis of the entire coding region

changeType: SNV, copy_number_variation

genomeBuild: GRCh38

genomicSourceClass: Germline

title: PGX Targeted Gene Panel - Sequencing Analysis

specimen: Specimen: identifier = http://example.org/identifiers/specimens#pgx-spec-001; status = available; type = Blood specimen (specimen); receivedTime = 2020-12-20 10:00:00+0000

date: 2021-01-01 01:01:10-0600

note:

Sequencing coverage of 100% achieved across all targeted regions.

\n

Metrics

-SequencingCoverageDescription
*100 % (Details: UCUM code% = '%')100% coverage of protein-coding and exon-splicing regions for all three genes.

genomicRegion

type: Studied

Locus

-Concept
*protein-coding and exon-splicing regions of CYP2C19
*protein-coding and exon-splicing regions of CYP2C9
*protein-coding and exon-splicing regions of VKORC1

genomicRegion

type: Called

Locus

-Concept
*CYP2C19
*CYP2C9
*VKORC1

Outputs

-FileType
*DocumentReference: identifier = http://example.org/identifiers/files#pgx-vcf-001; status = current; docStatus = final; description = VCF file containing PGX variant calls for CYP2C19, CYP2C9, and VKORC1; securityLabel = RestrictedVCF

Performers

-ActorRole
*Practitioner Jane Doel Performer

Devices

-DeviceFunction
*Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object)Sequencing
"^^rdf:XMLLiteral ] ] ; # fhir:identifier ( [ fhir:use [ fhir:v "temp" ] ; fhir:system [ fhir:v "http://example.org/identifiers/genomicstudies"^^xsd:anyURI ; fhir:l ] ; fhir:value [ fhir:v "urn:uuid:pgx-study-0001" ] ] ) ; # # Pharmacogenomics (PGX) targeted gene panel study. # Germline sequencing of CYP2C19, CYP2C9, and VKORC1 protein-coding and # exon-splicing regions to guide drug dosing decisions. # Demonstrates: coded gene genomicRegion.studied (HGNC), genomicRegion.called, metrics (sequencing coverage), # germline genomicSourceClass. # fhir:status [ fhir:v "available"] ; # fhir:type ( [ fhir:coding ( [ a sct:405825005 ; fhir:system [ fhir:v "http://snomed.info/sct"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "405825005" ] ; fhir:display [ fhir:v "Molecular genetic test (procedure)" ] ] ) ] ) ; # fhir:subject [ fhir:l ; fhir:reference [ fhir:v "Patient/pgxPatient" ] ] ; # fhir:startDate [ fhir:v "2021-01-01"^^xsd:date] ; # fhir:basedOn ( [ fhir:l ; fhir:reference [ fhir:v "ServiceRequest/pgxServiceRequest" ] ] ) ; # fhir:interpreter ( [ fhir:l ; fhir:reference [ fhir:v "Practitioner/practitioner02" ] ] ) ; # fhir:reason ( [ fhir:concept [ fhir:coding ( [ a sct:182992009 ; fhir:system [ fhir:v "http://snomed.info/sct"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "182992009" ] ; fhir:display [ fhir:v "Treatment completed (situation)" ] ] ) ] ] ) ; # fhir:note ( [ fhir:text [ fhir:v "PGX panel ordered prior to initiating warfarin therapy to guide dosing based on CYP2C9 and VKORC1 genotype." ] ] ) ; # fhir:description [ fhir:v "Pharmacogenomics sequencing panel targeting protein-coding and exon-splicing regions of CYP2C19, CYP2C9, and VKORC1 to inform drug selection and dosing."] ; # fhir:analysis ( [ fhir:identifier ( [ fhir:use [ fhir:v "temp" ] ; fhir:system [ fhir:v "http://example.org/identifiers/genomicAnalyses"^^xsd:anyURI ; fhir:l ] ; fhir:value [ fhir:v "urn:uuid:pgx-analysis-0001" ] ] ) ; fhir:methodType ( [ fhir:coding ( [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "sequence-analysis-of-the-entire-coding-region" ] ; fhir:display [ fhir:v "Sequence analysis of the entire coding region" ] ] ) ] ) ; fhir:changeType ( [ fhir:coding ( [ fhir:system [ fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "SO:0001483" ] ; fhir:display [ fhir:v "SNV" ] ] ) ] [ fhir:coding ( [ fhir:system [ fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "SO:0001019" ] ; fhir:display [ fhir:v "copy_number_variation" ] ] ) ] ) ; fhir:genomeBuild [ fhir:coding ( [ a loinc:LA26806-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "LA26806-2" ] ; fhir:display [ fhir:v "GRCh38" ] ] ) ] ; fhir:genomicSourceClass [ fhir:coding ( [ a loinc:LA6683-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "LA6683-2" ] ; fhir:display [ fhir:v "Germline" ] ] ) ] ; fhir:title [ fhir:v "PGX Targeted Gene Panel - Sequencing Analysis" ] ; fhir:specimen ( [ fhir:l ; fhir:reference [ fhir:v "Specimen/pgxSpecimen" ] ] ) ; fhir:date [ fhir:v "2021-01-01T01:01:10-06:00"^^xsd:dateTime ] ; fhir:note ( [ fhir:text [ fhir:v "Sequencing coverage of 100% achieved across all targeted regions." ] ] ) ; fhir:metrics [ fhir:sequencingCoverage [ fhir:value [ fhir:v "100"^^xsd:decimal ] ; fhir:unit [ fhir:v "%" ] ; fhir:system [ fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "%" ] ] ; fhir:description [ fhir:v "100% coverage of protein-coding and exon-splicing regions for all three genes." ] ] ; fhir:genomicRegion ( [ fhir:type [ fhir:coding ( [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "studied" ] ; fhir:display [ fhir:v "Studied" ] ] ) ] ; fhir:locus ( [ fhir:concept [ fhir:coding ( [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "HGNC:2621" ] ; fhir:display [ fhir:v "CYP2C19" ] ] ) ; fhir:text [ fhir:v "protein-coding and exon-splicing regions of CYP2C19" ] ] ] [ fhir:concept [ fhir:coding ( [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "HGNC:2623" ] ; fhir:display [ fhir:v "CYP2C9" ] ] ) ; fhir:text [ fhir:v "protein-coding and exon-splicing regions of CYP2C9" ] ] ] [ fhir:concept [ fhir:coding ( [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "HGNC:23663" ] ; fhir:display [ fhir:v "VKORC1" ] ] ) ; fhir:text [ fhir:v "protein-coding and exon-splicing regions of VKORC1" ] ] ] ) ] [ fhir:type [ fhir:coding ( [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "called" ] ; fhir:display [ fhir:v "Called" ] ] ) ] ; fhir:locus ( [ fhir:concept [ fhir:coding ( [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "HGNC:2621" ] ; fhir:display [ fhir:v "CYP2C19" ] ] ) ] ] [ fhir:concept [ fhir:coding ( [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "HGNC:2623" ] ; fhir:display [ fhir:v "CYP2C9" ] ] ) ] ] [ fhir:concept [ fhir:coding ( [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "HGNC:23663" ] ; fhir:display [ fhir:v "VKORC1" ] ] ) ] ] ) ] ) ; # genomicRegion: studied = all three PGx gene targets (protein-coding and exon-splicing regions) fhir:output ( [ fhir:file [ fhir:l ; fhir:reference [ fhir:v "DocumentReference/pgxVCFfile" ] ] ; fhir:type [ fhir:coding ( [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "vcf" ] ; fhir:display [ fhir:v "VCF" ] ] ) ] ] ) ; fhir:performer ( [ fhir:actor [ fhir:l ; fhir:reference [ fhir:v "Practitioner/practitioner02" ] ] ; fhir:role [ fhir:coding ( [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v3-ParticipationType"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "PRF" ] ; fhir:display [ fhir:v "Performer" ] ] ) ] ] ) ; fhir:device ( [ fhir:device [ fhir:l ; fhir:reference [ fhir:v "Device/NGS-device" ] ] ; fhir:function [ fhir:coding ( [ a loinc:LA26398-0 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "LA26398-0" ] ; fhir:display [ fhir:v "Sequencing" ] ] ) ] ] ) ] ) . # a fhir:Uv . a fhir:Uv . a fhir:Uv . a fhir:Uv . a fhir:Uv . a fhir:Uv . # -------------------------------------------------------------------------------------