Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 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
Generated Narrative: Bundle bundle-pgxexample
Bundle bundle-pgxexample of type transaction
Entry 1 - fullUrl = http://example.org/fhir/DiagnosticReport/pgx-report
Resource DiagnosticReport:
Generated Narrative: DiagnosticReport pgx-report
Genetic analysis report (Genetics)
Subject Anonymous Patient (no stated gender), DoB Unknown When For 2016 Reported 2018-03-06 00:00:00-0500 Performer Organization Some lab Report Details
Code Value
Request:
POST DiagnosticReport
Entry 2 - fullUrl = http://example.org/fhir/Patient/ExamplePatient
Resource Patient:
This would contain patient identifiers, demographics, etc.
Request:
POST Patient
Entry 3 - fullUrl = http://example.org/fhir/Specimen/ExampleSpecimen
Resource Specimen:
Generated Narrative: Specimen ExampleSpecimen
Request:
POST Specimen
Entry 4 - fullUrl = http://example.org/fhir/Organization/ExampleLab
Resource Organization:
Generated Narrative: Organization ExampleLab
name: Some lab
Request:
POST Organization
Entry 5 - fullUrl = http://example.org/fhir/ServiceRequest/pgx-request
Resource ServiceRequest:
Generated Narrative: ServiceRequest pgx-request
status: Active
intent: Original Order
code: Genetic analysis report
subject: Anonymous Patient (no stated gender), DoB Unknown
reasonCode: Worried about family planning
Request:
POST ServiceRequest
Entry 6 - fullUrl = http://example.org/fhir/Observation/med-impact-pgx-example
Resource Observation:
Generated Narrative: Observation med-impact-pgx-example
status: Final
category: Laboratory, Genetics
code: Therapeutic Implication
subject: Anonymous Patient (no stated gender), DoB Unknown
effective: 2018
issued: 2018-03-06 00:00:00-0500
performer: Organization Some lab
derivedFrom: Bundle: type = transaction
component
code: Therapeutic Implication
value: Rapid metabolizer
component
code: Medication assessed
value: mercaptopurine
Request:
POST Observation
Entry 7 - fullUrl = http://example.org/fhir/Observation/genotype-pgx-example
Resource Observation:
Generated Narrative: Observation genotype-pgx-example
status: Final
category: Laboratory, Genetics
code: genotype display name
subject: Anonymous Patient (no stated gender), DoB Unknown
effective: 2018
issued: 2018-03-06 00:00:00-0500
performer: Organization Some lab
value: CYP2C9 *4/*35B
specimen: Specimen
derivedFrom:
Components
Code Value[x] Gene studied ID CYP2C9
Request:
POST Observation
Entry 8 - fullUrl = http://example.org/fhir/Observation/haplotype-1-pgx-example
Resource Observation:
Generated Narrative: Observation haplotype-1-pgx-example
status: Final
category: Laboratory, Genetics
code: Haplotype Name
subject: Anonymous Patient (no stated gender), DoB Unknown
effective: 2018
issued: 2018-03-06 00:00:00-0500
performer: Organization Some lab
value: CYP2C9 *35B
specimen: Specimen
derivedFrom: Bundle: type = transaction
Components
Code Value[x] Gene studied ID CYP2C9
Request:
POST Observation
Entry 9 - fullUrl = http://example.org/fhir/Observation/haplotype-2-pgx-example
Resource Observation:
Generated Narrative: Observation haplotype-2-pgx-example
status: Final
category: Laboratory, Genetics
code: Haplotype Name
subject: Anonymous Patient (no stated gender), DoB Unknown
effective: 2018
issued: 2018-03-06 00:00:00-0500
performer: Organization Some lab
value: CYP2C9 *4
specimen: Specimen
derivedFrom: Bundle: type = transaction
Components
Code Value[x] Gene studied ID CYP2C9
Request:
POST Observation
Entry 10 - fullUrl = http://example.org/fhir/Observation/variant-1-pgx-example
Resource Observation:
Generated Narrative: Observation variant-1-pgx-example
status: Final
category: Laboratory, Genetics
code: Genetic variant assessment
subject: Anonymous Patient (no stated gender), DoB Unknown
effective: 2018
issued: 2018-03-06 00:00:00-0500
performer: Organization Some lab
value: Present
specimen: Specimen
derivedFrom: Bundle: type = transaction
component
code: Gene studied ID
value: CYP2C9
component
code: Discrete genetic variant
value: rs12345
component
code: Ref nucleotide
value: T
component
code: Alt allele
value: G
component
code: Genomic allele start-end
value: 55227976-55227977
Request:
POST Observation
Entry 11 - fullUrl = http://example.org/fhir/Observation/variant-2-pgx-example
Resource Observation:
Generated Narrative: Observation variant-2-pgx-example
status: Final
category: Laboratory, Genetics
code: Genetic variant assessment
subject: Anonymous Patient (no stated gender), DoB Unknown
effective: 2018
issued: 2018-03-06 00:00:00-0500
performer: Organization Some lab
value: Present
specimen: Specimen
derivedFrom: Bundle: type = transaction
component
code: Gene studied ID
value: CYP2C9
component
code: Genomic reference sequence ID
value: NG_007726.3
component
code: Discrete genetic variant
value: rs233455
component
code: Ref nucleotide
value: T
component
code: Alt allele
value: G
component
code: Genomic allele start-end
value: 55227978-55227979
Request:
POST Observation
Entry 12 - fullUrl = http://example.org/fhir/MolecularSequence/sequence-1-pgx-example
Resource MolecularSequence:
Generated Narrative: MolecularSequence sequence-1-pgx-example
type: DNA Sequence
coordinateSystem: 0
ReferenceSeqs
Orientation ReferenceSeqId WindowStart WindowEnd Sense orientation of referenceSeq NG-007726.3 55227970 55227980
Request:
POST MolecularSequence
Entry 13 - fullUrl = http://example.org/fhir/MolecularSequence/sequence-2-pgx-example
Resource MolecularSequence:
Generated Narrative: MolecularSequence sequence-2-pgx-example
type: DNA Sequence
coordinateSystem: 0
ReferenceSeqs
Orientation ReferenceSeqId WindowStart WindowEnd Sense orientation of referenceSeq NG-007726.3 55227970 55227980
Request:
POST MolecularSequence
Entry 14 - fullUrl = http://example.org/fhir/Task/med-usage-impact-task-pgx-example
Resource Task:
Generated Narrative: Task med-usage-impact-task-pgx-example
status: Requested
intent: proposal
code: Any Increase does Recommendation Text from the provider
description: Any Increase does Recommendation Text from the provider
focus: Bundle: type = transaction
for: Anonymous Patient (no stated gender), DoB Unknown
reasonReference: Bundle: type = transaction
Request:
POST Task
Entry 15 - fullUrl = http://example.org/fhir/MedicationStatement/current-med-example
Resource MedicationStatement:
Generated Narrative: MedicationStatement current-med-example
status: Unknown
medication: mercaptopurine
Request:
POST MedicationStatement
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-11-24
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