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-specific-variants | Version: 3.0.1-SNAPSHOT | |||
| Active as of 2024-04-09 | Computable Name: FindSubjectSpecificVariants | |||
Determine if specified simple variants are present.
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).
Parameters
| Use | Name | Scope | Cardinality | Type | Binding | Documentation |
| IN | subject | 1..1 | string (reference) | The subject of interest. | ||
| IN | variants | 1..* | string (string) | List of variants being sought. Must be in HGVS or SPDI format. | ||
| 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. | ||
| OUT | variants | 1..* | (one for each variant in variantList) | |||
| OUT | variants.variantItem | 1..1 | string | variant from variantList | ||
| OUT | variants.presence | 1..1 | boolean | |||
| OUT | variants.variant | 0..* | 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. |
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 |
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.
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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