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-haplotypes | Version: 3.0.0 | |||
Active as of 2024-11-24 | Computable Name: FindSubjectHaplotypes |
Retrieve haplotypes/genotypes for specified genes.
Generated Narrative: OperationDefinition find-subject-haplotypes
Use | Name | Scope | Cardinality | Type | Binding | Documentation |
IN | subject | 1..1 | string (reference) | The subject of interest. | ||
IN | genes | 1..* | string (token) | List of genes to be searched. Must be in token or codesystem|code 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 haplotypes irrespective of genomic source class. | ||
OUT | haplotypes | 1..* | (one for each gene in geneList) | |||
OUT | haplotypes.geneItem | 1..1 | string | gene from geneList | ||
OUT | haplotypes.haplotype | 0..* | Observation | Haplotypes must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype]. | ||
OUT | haplotypes.genotype | 0..* | Observation | Genotypes must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype]. |
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 |
CYP2D6 haplotypes?
$find-subject-haplotypes?subject=HG00403&genes=http://www.genenames.org|HGNC:2625
Haplotypes that include HLA-A or HLA-B?
$find-subject-haplotypes?subject=HG00403&genes=http://www.genenames.org|HGNC:4931,http://www.genenames.org|HGNC:4932
Patient HG00403 underwent preemptive pharmacogenomic testing. Clinician now wants to prescribe amitriptyline, but first wants to see CYP2D6 and CYP2C19 star alleles.