Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 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-intersecting-variants | Version: 3.0.0 | |||
| Active as of 2024-11-19 | Computable Name: FindSubjectStructuralIntersectingVariants | |||
Determine if structural variants are present that overlap range(s).
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).
Generated Narrative: OperationDefinition find-subject-structural-intersecting-variants
| 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. |
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 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.
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-11-19
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