Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot
Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot
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
| Official URL: http://hl7.org/fhir/uv/genomics-reporting/OperationDefinition/find-subject-structural-subsuming-variants | Version: 3.0.1-SNAPSHOT | |||
| Active as of 2024-04-09 | Computable Name: FindSubjectStructuralSubsumingVariants | |||
Determine if structural variants are present that fully subsume a range.
Determine if structural variants are present that fully subsume a range. (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 subsumes the range | ||
| OUT | variants.variant | 0..* | Observation | If includeVariants=true then include variants that subsume 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. |
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 a tumor recurrence. WES of new mass (specimen1) is performed. Clinical trial inclusion criteria includes somatic MET amplification. See if patient HG00403 has a structural variant that subsumes MET (NC_000007.14:116672195-116798386) in specimen1.
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.1-SNAPSHOT based on FHIR 4.0.1. Generated 2024-04-09
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