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 Subject Variants

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

Determine if simple variants are present that overlap range(s).

### Description

Determine if simple variants are present that overlap range(s). (See section 'Simple vs. Structural variant operations' for the distinction between simple and structural variants).

### Parameters

Use | Name | Scope | Cardinality | Type | Binding | Documentation
IN | subject |  | 1..1 | string (reference) |  | The subject of interest.
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 | testIdentifiers |  | 0..* | string (token) |  | Supply a list of test identifiers. Only results originating from one of these tests will be returned.
IN | testDateRange |  | 0..1 | Period |  | Supply a date range. Only results generated during this range will be returned.
IN | specimenIdentifiers |  | 0..* | string (token) |  | Supply a list of specimen identifiers. Only results derived from one of these specimens will be returned.
IN | genomicSourceClass |  | 0..1 | code |  | Enables an App to limit results to those that are 'germline' or 'somatic'. Default is to include variants irrespective of genomic source class.
IN | includeVariants |  | 0..1 | boolean |  | Include variants in response if set to true. Default=false.
IN | includePhasing |  | 0..1 | boolean |  | If true, then assume includeVariants=true, and return variants and sequence-phase-relationships between returned variants. Default=false.
OUT | variants |  | 1..* |  |  | (one for each range in rangeList)
OUT | variants.rangeItem |  | 1..1 | string |  | range from rangeList
OUT | variants.presence |  | 1..1 | boolean |  | True if as least one variant is identified in the range
OUT | variants.variant |  | 0..* | Observation |  | If includeVariants=true then include variants in the range. Variants must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant] and minimally include valueCodeableConcept; component:genomic-ref-seq; component:ref-allele; component:alt-allele; component:coordinate-system (valued with '0-based interval counting'); component:exact-start-end.
OUT | variants.sequencePhaseRelationship |  | 0..* | Observation |  | If includePhasing=true and includeVariants=true then include sequence-phase-relationships between returned variants. Sequence phase relationships must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition-sequence-phase-relationship.html] and minimally include valueCodeableConcept and 2..2 derivedFrom:variant references.

### 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

Patient HG00403 has WES of a tumor biopsy specimen. See if patient HG00403 had any simple somatic variants detected in BRAF (NC_000007.14:140713327-140924929) or ERBB2 (NC_000017.11:39688093-39728660) by test1.

    GET .../$find-subject-variants?subject=HG00403&ranges=NC_000007.14:140713327-140924929,NC_000017.11:39688093-39728660&testIdentifiers=test1&genomicSourceClass=somatic&includeVariants=true

See example output.