Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions
| Official URL: http://hl7.org/fhir/uv/genomics-reporting/OperationDefinition/find-subject-variants | Version: 3.0.0-ballot | |||
| Active as of 2023-12-18 | Computable Name: FindSubjectVariants | |||
Determine if simple variants are present that overlap range(s).
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. |
Contents:
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 |
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.
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0-ballot based on FHIR 4.0.1. Generated 2023-12-18
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