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

## OperationDefinition: Find Subject Haplotypes

Official URL: http://hl7.org/fhir/uv/genomics-reporting/OperationDefinition/find-subject-haplotypes | Version: 4.0.0-cibuild
Standards status: Trial-use | Maturity Level: 2 | 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).

### Parameters

Use | Name | Scope | Cardinality | Type | Binding | Documentation
IN | subject |  | 1..1 | string (reference) |  | The subject of interest.
IN | genes |  | 1..* | string (token) |  | List of genes to be searched. Must be in token or codesystem|code format.
IN | testIdentifiers |  | 0..* | string (token) |  | Supply a list of test identifiers. Only results originating from one of these tests will be returned.
IN | testDateRange |  | 0..1 | Period |  | Supply a date range. Only results generated during this range will be returned.
IN | specimenIdentifiers |  | 0..* | string (token) |  | Supply a list of specimen identifiers. Only results derived from one of these specimens will be returned.
IN | genomicSourceClass |  | 0..1 | string (token) |  | Enables an App to limit results to those that are 'germline' or 'somatic'. Default is to include haplotypes irrespective of genomic source class.
OUT | haplotypes |  | 1..* |  |  | (one for each gene in geneList)
OUT | haplotypes.geneItem |  | 1..1 | string |  | gene from geneList
OUT | haplotypes.haplotype |  | 0..* | Observation |  | Haplotypes must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype].
OUT | haplotypes.genotype |  | 0..* | 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.

    GET .../$find-subject-haplotypes?subject=HG00403&genes=http://www.genenames.org|HGNC:2625,http://www.genenames.org|HGNC:2621

See example output.