<specimen> <reference value="Specimen/pgxSpecimen"/> </specimen> <date value="2021-01-01T01:01:10-06:00"/> <note> <text value="Sequencing coverage of 100% achieved across all targeted regions."/> </note> <metrics> <sequencingCoverage> <value value="100"/> <unit value="%"/> <system value="http://unitsofmeasure.org"/> <code value="%"/> </sequencingCoverage> <description value="100% coverage of protein-coding and exon-splicing regions for all three genes."/> </metrics>  <genomicRegion> <type> <coding> <system value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype"/> <code value="studied"/> <display value="Studied"/> </coding> </type> <locus> <concept> <coding> <system value="http://www.genenames.org"/> <code value="HGNC:2621"/> <display value="CYP2C19"/> </coding> <text value="protein-coding and exon-splicing regions of CYP2C19"/> </concept> </locus> <locus> <concept> <coding> <system value="http://www.genenames.org"/> <code value="HGNC:2623"/> <display value="CYP2C9"/> </coding> <text value="protein-coding and exon-splicing regions of CYP2C9"/> </concept> </locus> <locus> <concept> <coding> <system value="http://www.genenames.org"/> <code value="HGNC:23663"/> <display value="VKORC1"/> </coding> <text value="protein-coding and exon-splicing regions of VKORC1"/> </concept> </locus> </genomicRegion>  <genomicRegion> <type> <coding> <system value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype"/> <code value="called"/> <display value="Called"/> </coding> </type> <locus> <concept> <coding> <system value="http://www.genenames.org"/> <code value="HGNC:2621"/> <display value="CYP2C19"/> </coding> </concept> </locus> <locus> <concept> <coding> <system value="http://www.genenames.org"/> <code value="HGNC:2623"/> <display value="CYP2C9"/> </coding> </concept> </locus> <locus> <concept> <coding> <system value="http://www.genenames.org"/> <code value="HGNC:23663"/> <display value="VKORC1"/> </coding> </concept> </locus> </genomicRegion> <output> <file> <reference value="DocumentReference/pgxVCFfile"/> </file> <type> <coding> <system value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"/> <code value="vcf"/> <display value="VCF"/> </coding> </type> </output> <performer> <actor> <reference value="Practitioner/practitioner02"/> </actor> <role> <coding> <system value="http://terminology.hl7.org/CodeSystem/v3-ParticipationType"/> <code value="PRF"/> <display value="Performer"/> </coding> </role> </performer> <device> <device> <reference value="Device/NGS-device"/> </device> <function> <coding> <system value="http://loinc.org"/> <code value="LA26398-0"/> <display value="Sequencing"/> </coding> </function> </device> </analysis> </GenomicStudy>

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.

description:

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

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.

Metrics
- SequencingCoverage Description
* 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
- File Type
* 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 = Restricted VCF
Performers
- Actor Role
* Practitioner Jane Doel Performer
Devices
- Device Function
* Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object) Sequencing