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 Specific Haplotypes

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

See if specified haplotypes/genotypes are present.

Description

See if specified haplotypes/genotypes are present.

Generated Narrative: OperationDefinition find-subject-specific-haplotypes

Parameters

UseNameScopeCardinalityTypeBindingDocumentation
INsubject1..1string
(reference)

The subject of interest.

INhaplotypes1..*string
(token)

List of haplotypes and/or genotypes being sought. 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 haplotype in haplotypeList)

OUThaplotypes.haplotypeItem1..1string

haplotype/genotype from haplotypeList

OUThaplotypes.presence1..1boolean
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

Are any of these haplotypes present [CYP2D6 *1/*5; CYP2D6 *1/*15; CYP2C19 *1/*2]?

$find-subject-specific-haplotypes?subject=HG00403&haplotypes=CYP2D6 *1/*5,CYP2D6 *1/*15,CYP2C19 *1/*2

Is haplotype [HLA-A*02:302+HLA-A*23:26/HLA-A*23:39^HLA-B*44:02:13+HLA-B*49:08] present?

$find-subject-specific-haplotypes?subject=HG00403&haplotypes=http://glstring.org|hla#3.33.0#HLA-A*02:302+HLA-A*23:26/HLA-A*23:39^HLA-B*44:02:13+HLA-B*49:08

Patient HG00403 underwent HLA typing, and clinician wants to know if there is any haplotype or genotype indication that HLA-A*23 is present.