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 Structural Intersecting Variants

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

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

### Description

Determine if structural variants are present that intersect range(s). (See section 'Use of genomic regions' for the distinction between variants that 'intersect' vs. 'subsume' a region; 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 | 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 | includeVariants |  | 0..1 | boolean |  | Include variants in response if set to true. 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 that intersects the range
OUT | variants.variant |  | 0..* | Observation |  | If includeVariants=true then include variants that intersect the range. Variants must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant] and minimally include valueCodeableConcept; component:coding-change-type; component:genomic-ref-seq; component:coordinate-system (valued with '0-based interval counting'); components outer-start-end and/or inner-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

Patient HG00403 has a tumor recurrence. WES of new mass (specimen1) is performed. Clinical trial inclusion criteria includes somatic EGFR exon 19 whole or partial deletions. See if patient HG00403 has a structural variant that intersects with EGFR exon 19 (NC_000007.13:55242414-55242513) in specimen1.

    GET .../$find-subject-structural-intersecting-variants?subject=HG00403&ranges=NC_000007.13:55242414-55242513&specimenIdentifiers=specimen1&genomicSourceClass=somatic&includeVariants=true

See example output.