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 Structural Subsuming Variants

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

Generated Narrative: OperationDefinition find-population-structural-subsuming-variants

Parameters

UseNameScopeCardinalityTypeBindingDocumentation
INranges1..*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').

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.rangeItem1..1string

range from rangeList

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

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.