Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot 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 3.0.1-SNAPSHOT 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

OperationDefinition: Find Subject Haplotypes

Official URL: http://hl7.org/fhir/uv/genomics-reporting/OperationDefinition/find-subject-haplotypes Version: 3.0.1-SNAPSHOT
Active as of 2024-07-15 Computable Name: FindSubjectHaplotypes

Retrieve haplotypes/genotypes for specified genes.

Description

Retrieve haplotypes/genotypes of specified genes.

Note to implementers: The committee is actively seeking feedback on the need to extend this operation to also support searching by region (e.g. to retrieve intergenic haplotypes).

Generated Narrative: OperationDefinition find-subject-haplotypes

Parameters

UseNameScopeCardinalityTypeBindingDocumentation
INsubject1..1string
(reference)

The subject of interest.

INgenes1..*string
(token)

List of genes to be searched. Must be in token or codesystem|code format.

INtestIdentifiers0..*string
(token)

Supply a list of test identifiers. Only results originating from one of these tests will be returned.

INtestDateRange0..1Period

Supply a date range. Only results generated during this range will be returned.

INspecimenIdentifiers0..*string
(token)

Supply a list of specimen identifiers. Only results derived from one of these specimens will be returned.

INgenomicSourceClass0..1string
(token)

Enables an App to limit results to those that are 'germline' or 'somatic'. Default is to include haplotypes irrespective of genomic source class.

OUThaplotypes1..*

(one for each gene in geneList)

OUThaplotypes.geneItem1..1string

gene from geneList

OUThaplotypes.haplotype0..*Observation

Haplotypes must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype].

OUThaplotypes.genotype0..*Observation

Genotypes must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype].

Notes:

Error Codes

Valid response codes are shown in the following table. Additional response codes (e.g. 5xx server error) may also be encountered.

Response Code Description
200 Successfully executed request
400 ERROR: Invalid query parameters
404 ERROR: Patient not found
422 ERROR: Failed LiftOver

Examples

CYP2D6 haplotypes?

$find-subject-haplotypes?subject=HG00403&genes=http://www.genenames.org|HGNC:2625

Haplotypes that include HLA-A or HLA-B?

$find-subject-haplotypes?subject=HG00403&genes=http://www.genenames.org|HGNC:4931,http://www.genenames.org|HGNC:4932

Patient HG00403 underwent preemptive pharmacogenomic testing. Clinician now wants to prescribe amitriptyline, but first wants to see CYP2D6 and CYP2C19 star alleles.