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 Structural Subsuming Variants

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

Retrieve count or list of patients having structural subsuming variants in specified regions.

### Description

Retrieve count or list of patients having structural subsuming variants in specified regions. (See section 'Genes vs. Regions' for the distinction between variants that 'intersect' vs. 'subsume' a region).

A patient meets numerator criteria if they have at least one structural variant subsuming a given range.

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.

### Parameters

Use | Name | Scope | Cardinality | Type | Binding | Documentation
IN | ranges |  | 1..* | string (special) |  | List of regions to be searched for variants. Must be in zero-based RefSeq:Integer-range format (e.g. 'NC_000007.14:55174721-55174820').
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.rangeItem |  | 1..1 | string |  | range from rangeList
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

A pharmacogeneticist is studying the accuracy of CYP2D6*5 (whole gene deletion) calling, and wants to compare cases where a structural variant caller indicates a whole gene deletion of CYP2D6 (NC_000022.10:42522500-42526812) against a pipeline used to report pharmacogenes.

To begin the process, the pharmacogeneticist identifies all patients that have structural variants subsuming CYP2D6.

    GET .../$find-population-structural-subsuming-variants?ranges=NC_000022.10:42522500-42526812&includePatientList=true

See example output.