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 Population Molecular Consequences

Official URL: http://hl7.org/fhir/uv/genomics-reporting/OperationDefinition/find-population-molecular-consequences Version: 3.0.1-SNAPSHOT
Active as of 2024-07-15 Computable Name: FindPopulationMolecularConsequences

Retrieve count or list of patients having molecular consequences.

Description

Retrieve count or list of patients having molecular consequences. More specifically, this operation retrieves the count +/- list of patients that have molecular consequences involving specific featureConsequences, derived from specific variants.

A patient meets numerator criteria if they have at least one molecular consequence matching the query parameters.

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

Population queries are designed to return a count of patients that match each item sought, with or without a list of patients matching the item(s) sought.

Generated Narrative: OperationDefinition find-population-molecular-consequences

Parameters

UseNameScopeCardinalityTypeBindingDocumentation
INvariants0..*string
(string)

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

INfeatureConsequences0..*string
(token)

List of consequences sought. Must be in token or codesystem|code format. (These will generally be coded with Sequence Ontology codes under SO:0001537)

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.

INincludePatientList0..1boolean

Include list of matching patients if set to true. Default=false.

OUTconsequences1..1
OUTconsequences.numerator1..1Quantity

Count of patients meeting criteria

OUTconsequences.denominator0..1Quantity

Count of patients in the cohort searched

OUTconsequences.subject0..*string

Patient ID. Include if includePatientList=true

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

As part of a quality assurance program, an oncologist seeks to identify patients harboring putative splice site variants in order to further assess disparities in molecularly guided treatment.