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 Diagnostic Implications

Official URL: http://hl7.org/fhir/uv/genomics-reporting/OperationDefinition/find-subject-dx-implications Version: 3.0.1-SNAPSHOT
Active as of 2024-07-15 Computable Name: FindSubjectDxImplications

Retrieves genetic diagnostic implications for variants.

Description

Retrieves genetic diagnostic implications for variants.

Generally, the operation will be called with 'subject' and 'ranges' parameters, which will return diagnostic implications for patient variants in supplied ranges. Another common pattern is to call the operation with just 'subject' and 'conditions' to do a broad sweep of the patient's variants for any associated with the supplied conditions; or with 'subject', 'ranges', and 'conditions' parameters, which will limit the return to diagnostic implications for the supplied conditions in supplied ranges - this is useful, for instance, to see if a patient has any variants in a given gene that are associated with a given disease. For other combinations of input parameters, the operation returns diagnostic implications satisfying all parameters.

Where no variants, ranges, or conditions are provided, the operation returns no implications.

As shown in the following picture, this operation can return previously instantiated implications and/or dynamically computed implications. Specific implementations can indicate their capabilities using a FHIR Capability Statement. Rules around the retention of dynamically computed implications are outside the scope of this operation, but a server could potentially instantiate those results based on the Therapeutic Implication, Diagnostic Implication, or Molecular Consequence FHIR profiles.

Instantiated vs Dynamically Computed Implications

The committee is actively seeking feedback on the feasibility of using this operation to return dynamically computed implications of structural variants.

Generated Narrative: OperationDefinition find-subject-dx-implications

Parameters

UseNameScopeCardinalityTypeBindingDocumentation
INsubject1..1string
(reference)

The subject of interest.

INvariants0..*string
(string)

List of variants from which implications are derived. Must be in HGVS or SPDI format.

INranges0..*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').

INconditions0..*string
(token)

List of conditions for which implications are sought. Must be in token or codesystem|code format.

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..1string
(token)

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

OUTimplication0..*Observation

Implications must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication]. The target(s) of the implication's derivedFrom shall also be included in the response.

OUTvariant0..*Observation

Variants must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant].

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

Clinician seeks to determine if their patient has any diagnostic implications for familial hypercholesterolemia.

$find-subject-dx-implications?subject=HG00403&conditions=http://snomed.info/sct|398036000

Clinician now wants to further constrain results from the preceeding example, to only return variants in the LDLR gene (NC_000019.10:11089431-11133820) that are associated with familial hypercholesterolemia.

$find-subject-dx-implications?subject=HG00403&conditions=http://snomed.info/sct|398036000&ranges=NC_000019.10:11089431-11133820

Patient HG00403 has a germline variant in the RYR1 gene (NC_000019.10:38499669:C:T). What are the diagnostic implications of this variant? (Results indicate that the variant is pathogenic for Malignant Hyperthermia).