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 Subject Specific Variants

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

Generated Narrative: OperationDefinition find-subject-specific-variants

Parameters

UseNameScopeCardinalityTypeBindingDocumentation
INsubject1..1string
(reference)

The subject of interest.

INvariants1..*string
(string)

List of variants being sought. Must be in HGVS or SPDI format.

INtestIdentifiers0..*string
(token)

Supply a list of test identifiers. Only results originating from one of these tests will be returned.

INtestDateRange0..1Period

Supply a date range. Only results generated during this range will be returned.

INspecimenIdentifiers0..*string
(token)

Supply a list of specimen identifiers. Only results derived from one of these specimens will be returned.

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.

OUTvariants1..*

(one for each variant in variantList)

OUTvariants.variantItem1..1string

variant from variantList

OUTvariants.presence1..1boolean
OUTvariants.variant0..*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.