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 Variants

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

Generated Narrative: OperationDefinition find-subject-variants

Parameters

UseNameScopeCardinalityTypeBindingDocumentation
INsubject1..1string
(reference)

The subject of interest.

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').

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..1code

Enables an App to limit results to those that are 'germline' or 'somatic'. Default is to include variants irrespective of genomic source class.

INincludeVariants0..1boolean

Include variants in response if set to true. Default=false.

INincludePhasing0..1boolean

If true, then assume includeVariants=true, and return variants and sequence-phase-relationships between returned variants. Default=false.

OUTvariants1..*

(one for each range in rangeList)

OUTvariants.rangeItem1..1string

range from rangeList

OUTvariants.presence1..1boolean

True if as least one variant is identified in the range

OUTvariants.variant0..*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.

OUTvariants.sequencePhaseRelationship0..*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.