Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build 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 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 Population Specific Haplotypes

Official URL: http://hl7.org/fhir/uv/genomics-reporting/OperationDefinition/find-population-specific-haplotypes Version: 4.0.0-cibuild
Standards status: Trial-use Maturity Level: 2 Computable Name: FindPopulationSpecificHaplotypes

Retrieve count or list of patients having specified genotypes/haplotypes.

Description

Retrieve count or list of patients having specified genotypes/haplotypes.

Population queries are designed to return a count of patients that match each item sought, with or without a list of patients matching the item(s) sought. As described in general guidance, the population denominator can be limited by referencing a FHIR Group instance.

As described in general guidance, FHIR Genomics Operations do not support 'AND' logic unless stated otherwise. This particular operation supports a logical 'AND' of the 'haplotypes' parameter, specified by repeating the parameter. 'AND' logic is useful when searching for other subjects sharing a specific constellation of haplotypes, as in the following example that seeks patients having haplotype 'a' or 'b' or 'c', and haplotype 'd' or 'e' or 'f', and haplotype 'i' or 'j' or 'k':

...&haplotypes=a,b,c&haplotypes=d,e,f&haplotypes=i,j,k

Parameters

UseNameScopeCardinalityTypeBindingDocumentation
INhaplotypes1..*string
(token)

List of haplotypes and/or genotypes being sought. Must be in token or codesystem|code format.

INgenomicSourceClass0..1string
(token)

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

INgroup0..1string
(reference)

Identifier of a FHIR Group. If supplied, the search is restricted to members of the group: numerator counts only group members, denominator is the number of members in the group, and the subject list (if includePatientList=true) contains only group members. If omitted, all patients in the repository are searched. An unknown group identifier results in an error.

INincludePatientList0..1boolean

Include list of matching patients if set to true. Default=false.

OUThaplotypes1..*

(one for each haplotype in haplotypeList)

OUThaplotypes.haplotypeItem1..1string

haplotype/genotype from haplotypeList

OUThaplotypes.numerator1..1Quantity

Count of patients having this variant (limited to members of group, if supplied)

OUThaplotypes.denominator0..1Quantity

Count of patients in the cohort searched (the number of members in group, if supplied; otherwise all patients in the repository)

OUThaplotypes.subject0..*string

Patient ID. Include if includePatientList=true. Limited to members of group, if supplied

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: Group not found
422 ERROR: Failed LiftOver

Examples

A transplant specialist is looking for potential unrelated donors in the donor registry that are a perfect HLA match for their patient.

GET .../$find-population-specific-haplotypes?haplotypes=A*1&haplotypes=B*8&haplotypes=DRB1*03&haplotypes=DRB3*01&haplotypes=A*31&haplotypes=B*35&haplotypes=DRB1*04&haplotypes=DRB4*01:02&includePatientList=true

See example output.