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-population-specific-variants | Version: 3.0.1-SNAPSHOT | |||
| Active as of 2024-04-09 | Computable Name: FindPopulationSpecificVariants | |||
Retrieve count or list of patients having specified variants.
Retrieve count or list of patients having specified variants.
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.
As described in general guidance, FHIR Genomics Operations do not support 'AND' logic unless stated otherwise. This particular operation supports a logical 'AND' of the 'variants' parameter, specified by repeating the parameter. 'AND' logic is useful when searching for other subjects sharing a specific constellation of variants, as in the following example that seeks patients having variant 'a' or 'b' or 'c', and variant 'd' or 'e' or 'f', and variant 'i' or 'j' or 'k':
...&variants=a,b,c&variants=d,e,f&variants=i,j,k
Parameters
| Use | Name | Scope | Cardinality | Type | Binding | Documentation |
| IN | variants | 1..* | string (string) | List of variants being sought. Must be in HGVS or SPDI format. | ||
| 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 | includePatientList | 0..1 | boolean | Include list of matching patients if set to true. Default=false. | ||
| OUT | variants | 1..* | ||||
| OUT | variants.variantItem | 1..1 | string | variant from variantList | ||
| OUT | variants.numerator | 1..1 | Quantity | Count of patients having this variant | ||
| OUT | variants.denominator | 0..1 | Quantity | Count of patients in the cohort searched | ||
| OUT | variants.subject | 0..* | string | Patient ID. Include if includePatientList=true |
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 |
An oncologist treating a patient with metastatic breast cancer determines the patient has the following somatic oncogenic mutations [NC_000010.10:g.121551307G>A, NC_000011.10:g.8263343T>C, NC_000001.10:g.198742263G>A], and wants to see if there are other patients that have ALL of these variants.
In the same scenario, the oncologist now wants to see if there are other patients that have ANY of these variants.
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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