{ "resourceType" : "GenomicStudy", "resourceDefinition" : "http://hl7.org/fhir/StructureDefinition/GenomicStudy|0.1.0-ci-build", "id" : "example-pgx", "language" : "en", "text" : { "status" : "generated", "div" : "

Generated Narrative: GenomicStudy example-pgx

Language: en

identifier: http://example.org/identifiers/genomicstudies/urn:uuid:pgx-study-0001\u00a0(use:\u00a0temp,\u00a0)

status: Available

type: Molecular genetic test (procedure)

subject: Adam B. Everyman (official) Male, DoB: 1951-01-20 ( Medical record number: m123\u00a0(use:\u00a0usual,\u00a0period:\u00a02021-01-01 --> (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\u00a0(use:\u00a0temp,\u00a0)

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
" }, "identifier" : [{ "use" : "temp", "system" : "http://example.org/identifiers/genomicstudies", "value" : "urn:uuid:pgx-study-0001" }], "status" : "available", "type" : [{ "coding" : [{ "system" : "http://snomed.info/sct", "code" : "405825005", "display" : "Molecular genetic test (procedure)" }] }], "subject" : { "reference" : "Patient/pgxPatient" }, "startDate" : "2021-01-01", "basedOn" : [{ "reference" : "ServiceRequest/pgxServiceRequest" }], "interpreter" : [{ "reference" : "Practitioner/practitioner02" }], "reason" : [{ "concept" : { "coding" : [{ "system" : "http://snomed.info/sct", "code" : "182992009", "display" : "Treatment completed (situation)" }] } }], "note" : [{ "text" : "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" : [{ "use" : "temp", "system" : "http://example.org/identifiers/genomicAnalyses", "value" : "urn:uuid:pgx-analysis-0001" }], "methodType" : [{ "coding" : [{ "system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype", "code" : "sequence-analysis-of-the-entire-coding-region", "display" : "Sequence analysis of the entire coding region" }] }], "changeType" : [{ "coding" : [{ "system" : "http://www.sequenceontology.org", "code" : "SO:0001483", "display" : "SNV" }] }, { "coding" : [{ "system" : "http://www.sequenceontology.org", "code" : "SO:0001019", "display" : "copy_number_variation" }] }], "genomeBuild" : { "coding" : [{ "system" : "http://loinc.org", "code" : "LA26806-2", "display" : "GRCh38" }] }, "genomicSourceClass" : { "coding" : [{ "system" : "http://loinc.org", "code" : "LA6683-2", "display" : "Germline" }] }, "title" : "PGX Targeted Gene Panel - Sequencing Analysis", "specimen" : [{ "reference" : "Specimen/pgxSpecimen" }], "date" : "2021-01-01T01:01:10-06:00", "note" : [{ "text" : "Sequencing coverage of 100% achieved across all targeted regions." }], "metrics" : { "sequencingCoverage" : { "value" : 100, "unit" : "%", "system" : "http://unitsofmeasure.org", "code" : "%" }, "description" : "100% coverage of protein-coding and exon-splicing regions for all three genes." }, "genomicRegion" : [{ "type" : { "coding" : [{ "system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype", "code" : "studied", "display" : "Studied" }] }, "locus" : [{ "concept" : { "coding" : [{ "system" : "http://www.genenames.org", "code" : "HGNC:2621", "display" : "CYP2C19" }], "text" : "protein-coding and exon-splicing regions of CYP2C19" } }, { "concept" : { "coding" : [{ "system" : "http://www.genenames.org", "code" : "HGNC:2623", "display" : "CYP2C9" }], "text" : "protein-coding and exon-splicing regions of CYP2C9" } }, { "concept" : { "coding" : [{ "system" : "http://www.genenames.org", "code" : "HGNC:23663", "display" : "VKORC1" }], "text" : "protein-coding and exon-splicing regions of VKORC1" } }] }, { "type" : { "coding" : [{ "system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype", "code" : "called", "display" : "Called" }] }, "locus" : [{ "concept" : { "coding" : [{ "system" : "http://www.genenames.org", "code" : "HGNC:2621", "display" : "CYP2C19" }] } }, { "concept" : { "coding" : [{ "system" : "http://www.genenames.org", "code" : "HGNC:2623", "display" : "CYP2C9" }] } }, { "concept" : { "coding" : [{ "system" : "http://www.genenames.org", "code" : "HGNC:23663", "display" : "VKORC1" }] } }] }], "output" : [{ "file" : { "reference" : "DocumentReference/pgxVCFfile" }, "type" : { "coding" : [{ "system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat", "code" : "vcf", "display" : "VCF" }] } }], "performer" : [{ "actor" : { "reference" : "Practitioner/practitioner02" }, "role" : { "coding" : [{ "system" : "http://terminology.hl7.org/CodeSystem/v3-ParticipationType", "code" : "PRF", "display" : "Performer" }] } }], "device" : [{ "device" : { "reference" : "Device/NGS-device" }, "function" : { "coding" : [{ "system" : "http://loinc.org", "code" : "LA26398-0", "display" : "Sequencing" }] } }] }] }