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 Population Specific Variants

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

Retrieve count or list of patients having specified variants.

Description

Retrieve count or list of patients having specified variants.

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

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

Generated Narrative: OperationDefinition find-population-specific-variants

Parameters

UseNameScopeCardinalityTypeBindingDocumentation
INvariants1..*string
(string)

List of variants being sought. Must be in HGVS or SPDI 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.

INincludePatientList0..1boolean

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

OUTvariants1..*
OUTvariants.variantItem1..1string

variant from variantList

OUTvariants.numerator1..1Quantity

Count of patients having this variant

OUTvariants.denominator0..1Quantity

Count of patients in the cohort searched

OUTvariants.subject0..*string

Patient ID. Include if includePatientList=true

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

An oncologist treating a patient with metastatic breast cancer determines the patient has the following somatic oncogenic mutations [NC_000010.10:g.121551307G>A, NC_000011.10:g.8263343T>C, NC_000001.10:g.198742263G>A], and wants to see if there are other patients that have ALL of these variants.

In the same scenario, the oncologist now wants to see if there are other patients that have ANY of these variants.