Genomics Reporting Implementation Guide
3.0.0 - STU3 International flag

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

Example Bundle: bundle-pgxexample

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)

SubjectAnonymous Patient (no stated gender), DoB Unknown
When For2016
Reported2018-03-06 00:00:00-0500
Performer Organization Some lab

Report Details

CodeValue

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

subject: Anonymous Patient (no stated gender), DoB Unknown

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

-CodeValue[x]
*Gene studied IDCYP2C9

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

-CodeValue[x]
*Gene studied IDCYP2C9

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

-CodeValue[x]
*Gene studied IDCYP2C9

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

-OrientationReferenceSeqIdWindowStartWindowEnd
*Sense orientation of referenceSeqNG-007726.35522797055227980

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

-OrientationReferenceSeqIdWindowStartWindowEnd
*Sense orientation of referenceSeqNG-007726.35522797055227980

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

subject: Anonymous Patient (no stated gender), DoB Unknown

Request:

POST MedicationStatement