Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild 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

Bundle bundle-pgxexample of type transaction

Entry 1 - fullUrl = http://example.org/fhir/DiagnosticReport/pgx-report

Resource DiagnosticReport:

> Generated Narrative: DiagnosticReport pgx-report

> Profile: Genomic 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 | Flags | When For
> Therapeutic Implication |  | Final | 2018
> genotype display name | CYP2C9 *4/*35B | Final | 2018
> Haplotype Name | CYP2C9 *35B | Final | 2018
> Haplotype Name | CYP2C9 *4 | Final | 2018
> Genetic variant assessment | Present | Final | 2018
> Genetic variant assessment | Present | Final | 2018

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

> Profile: Therapeutic Implication

> 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: Observation genotype display name

> > 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

> Profile: Genotype

> 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:

> - Observation Haplotype Name
> - Observation Haplotype Name

> ### 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

> Profile: Haplotype

> 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: Observation Genetic variant assessment

> ### 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

> Profile: Haplotype

> 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: Observation Genetic variant assessment

> ### 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

> Profile: Variant

> 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: MolecularSequence: type = dna; coordinateSystem = 0

> > 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

> Profile: Variant

> 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: MolecularSequence: type = dna; coordinateSystem = 0

> > 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

> Profile: Medication Recommendation

> status: Requested

> intent: proposal

> code: Any Increase does Recommendation Text from the provider

> description: Any Increase does Recommendation Text from the provider

> focus: MedicationStatement: status = unknown; medication[x] = mercaptopurine

> for: Anonymous Patient (no stated gender), DoB Unknown

> reasonReference: Observation Therapeutic Implication

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