Data Mapping

Details regarding the data mapping for DGTS is provided below (only the subset mapped to FHIR has been represented here):

Genomic Test Package

Column Type Description FHIR Mapping - OM (Instance) FHIR Mapping - DGTS (Definition)
genomic_test_package_readable_id string A unique identifier for the genomic test package which is consistent between versions of the package. Has the prefix TP followed by an integer e.g. TP123. ServiceRequest.reasonCode.coding.code PlanDefinition.identifier
name string The name of the genomic test package. This is intended to allow users to quickly identify high-level information about the package like what disease it is related to. ServiceRequest.reasonCode.coding.display PlanDefinition.title
state string The current state of the package in the directory, like "Draft", "Live", "Deprecated" or "Retired. N/A PlanDefinition.status
version string Version of the package. ServiceRequest.reasonCode.coding.extension:code-version PlanDefinition.version
associated_legacy_clinical_indication_codes string Legacy R and M clinical indication codes that are associated with this package. PlanDefinition.identifier(use=old)

Links

Type Display Name Cardinality FHIR Mapping - OM (Instance) FHIR Mapping - DGTS (Definition)
GmsV2Modality GMS V2 Modality MANY N/A PlanDefinition.goal.description
GmsV2ClinicalSpecialty [GMS V2] Clinical Specialty MANY PractitionerRole.specialty PlanDefinition.useContext

Genomic Test

Column Type Description FHIR Mapping - OM (Instance) FHIR Mapping - DGTS (Definition)
additional_panels_available string Indicates whether a requester can request additional panels as part of their test request, must request at least one additional panel, or cannot request additional panels. N/A ActivityDefinition.library (Library.parameter(name:additional_panels_available) min and max values indicate requirement)
state string The current state of the package in the directory, like "Draft", "Live", "Deprecated" or "Retired". N/A ActivityDefinition.status
target_disease_required boolean Indicates whether the requester must provide the patient's disease as part of the information contained in the test request. Generally, required for multipurpose tests. A value of 1 indicates yes, 0 indicates no. ServiceRequest.reasonCode (if boolean true = captures actual target) ActivityDefinition.library (Library.parameter(name:target_disease_required) min and max values indicate requirement)
target_gene_required boolean Indicates whether the requester must provide the patient's target gene as part of the information contained in the test request. Generally, required for multipurpose tests. ServiceRequest.orderDetail (if boolean true = captures actual target) ActivityDefinition.library (Library.parameter(name:target_gene_required) min and max values indicate requirement)
target_variant_required boolean Indicates whether the requester must provide the patient's target variant as part of the information contained in the test request. Generally, required for multipurpose tests. ServiceRequest.orderDetail (if boolean true = captures actual target) ActivityDefinition.library (Library.parameter(name:target_variant_required) min and max values indicate requirement)
test_name string The name of the genomic test. This should convey high-level information about the text like targets or diseases depending on what the scope of the test is. ServiceRequest.code.coding.display ActivityDefinition.title
test_readable_id string A unique identifier for the genomic test which is consistent between versions of the package. Has the prefix GT followed by an integer e.g. GT123 ServiceRequest.code.coding.code ActivityDefinition.identifier
legacy_test_codes string Associated legacy test codes to enable searching by users. ActivityDefinition.identifier(use=old)

Links

Type Display Name Cardinality FHIR Mapping - OM (Instance) FHIR Mapping - DGTS (Definition)
GmsV2TestMethod GMS V2 Test Method ONE N/A ActivityDefinition.code
GmsV2GelPanel GMS V2 GEL Panel MANY ServiceRequest.orderDetail ActivityDefinition.relatedArtifact
GmsV2SampleType GMS V2 Sample Type MANY Specimen.type ActivityDefinition.specimenRequirement

Test Method

Column Type Description FHIR Mapping - DGTS (Definition)
method_name string The name of the test method. ActivityDefinition.code.coding.code

Sample Type

Column Type Description FHIR Mapping - DGTS (Definition)
sample_origin string Indicates whether a somatic or germline sample is required. SpecimenDefinition.typeCollected
sample_preference_status string Indicates the order of preference for this sample type for a particular test (e.g., "Required" "Preferred," "Accepted,"). This helps guide clinicians and labs on the most suitable sample to use for optimal results. A required sample type means this must be provided so that the test can be performed. A preferred sample types means that that is the most preferable for performing the test. An accepted sample type means that it’s acceptable for performing the test. SpecimenDefinition.typeTested.preference
sample_state string Specifies the state, medium or preservative for the sample such as fresh cells, EDTA, FFPE Slides SpecimenDefinition.typeTested.container.preparation/additive (exact mapping in pending alignment of the codelist to FHIR)
sample_type string A concise, unique name for the biological sample (e.g., "Blood," "Saliva," "Fresh Tissue"). SpecimenDefinition.typeTested.type

Modality

Column Type Description FHIR Mapping - DGTS (Definition)
modality_name string The name of the modality. PlanDefinition.goal.description.coding.code

GEL Panel

Column Type Description FHIR Mapping - DGTS (Definition)
panel_type array[string] A list of the panel types as described by PanelApp, such as Component of a Super Panel or Super Panel, GMS Rare Disease Virtual is the value that shows users that it can be added to the order as an additional panel Library.parameter