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 Specific Variants

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

Determine if specified simple variants are present.

### Description

Determine if specified simple variants are present or not. If any specified variant instance that passes the filters is present, then presence=true, else presence=false. (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 | variants |  | 1..* | string (string) |  | List of variants being sought. Must be in HGVS or SPDI format.
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 | 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.
OUT | variants |  | 1..* |  |  | (one for each variant in variantList)
OUT | variants.variantItem |  | 1..1 | string |  | variant from variantList
OUT | variants.presence |  | 1..1 | boolean |  |
OUT | variants.variant |  | 0..* | Observation |  | 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.

### 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

See if patient HG00403 had any of these [NM_001354609.2:c.1799T>A, NM_007294.4:c.5559C>A, NC_000001.10:g.12225351T>A, NM_000038.6:c.55G>T, NM_001354609.2:c.1802=] germline variants detected by test1 or test2.

    GET .../$find-subject-specific-variants?subject=HG00403&variants=NM_001354609.2:c.1799T>A,NM_007294.4:c.5559C>A,NC_000001.10:g.12225351T>A,NM_000038.6:c.55G>T,NM_001354609.2:c.1802=&testIdentifiers=test1,test2&genomicSourceClass=germline

See example output.