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 Population Specific Variants

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

### Parameters

Use | Name | Scope | Cardinality | Type | Binding | Documentation
IN | variants |  | 1..* | string (string) |  | List of variants being sought. Must be in HGVS or SPDI format.
IN | genomicSourceClass |  | 0..1 | string (token) |  | Enables an App to limit results to those that are 'germline' or 'somatic'. Default is to include variants irrespective of genomic source class.
IN | includePatientList |  | 0..1 | boolean |  | Include list of matching patients if set to true. Default=false.
OUT | variants |  | 1..* |  |  |
OUT | variants.variantItem |  | 1..1 | string |  | variant from variantList
OUT | variants.numerator |  | 1..1 | Quantity |  | Count of patients having this variant
OUT | variants.denominator |  | 0..1 | Quantity |  | Count of patients in the cohort searched
OUT | variants.subject |  | 0..* | 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.

    GET .../$find-population-specific-variants?variants=NC_000010.10:g.121551307G>A&variants=NC_000011.10:g.8263343T>C&variants=NC_000001.10:g.198742263G>A

See example output.

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

    GET .../$find-population-specific-variants?variants=NC_000010.10:g.121551307G>A,NC_000011.10:g.8263343T>C,NC_000001.10:g.198742263G>A

See example output.