Duo Trio Testing

The current modelling for Duo/Trio testing assumes a ServiceRequest for each participant, with each marked as either a proband or consultand request. Consultand's should be linked to the proband through RelatedPerson resources, added to ServiceRequest.supportingInfo on the consultand request. All requests SHALL use a shared Requisition Identifier to link the tests.

The Genomics Order Management service will create and maintain a RequestGroup for retrieving grouped requests.

The following steps is a walk through of:

1. Requester searches for a patient (a dummy patient has been pre-populated as an example)

Parameters:

given=Phoebe
family=Smitham
birthdate=eq2013-09-27

Response:

Patient-PheobeSmitham-Example

2. Requester selects appropriate code. In this scenario, the example used is Likely Inborn Metabolism (R98)

Saved under ServiceRequest.code

3. Requester completes the Test Order Form and indicates family members ROD and sample associated to the test request

POST of Test order transaction Bundle for Pheobe Smitham consisting of the following resources:

Patient-PheobeSmitham-Example

Observation-AutisticBehaviour-Example

Observation-DelayedSpeechLanguageDevt-Example

Observation-DiseasePenetrancePheobeSmitham-Example

Observation-IntellectualDisabilityProfound-Example

Observation-NonConsanguinousUnionProband-Example

Condition-InbornErrorOfMetabolism-Example

PractitionerRole-EugeneSmithLeedsSTH-Example

ServiceRequest-WGSTestOrderForm-TrioTestingProband-Example

Specimen-PheobeSmitham-Example

Details for Mother added to a linked consultand request:

Patient-PheobeSmithamMother-Example

RelatedPerson-AliceSmithamProbandMother-Example

Specimen-PheobeSmithamMother-Example

Observation-NonConsanguinousUnionProbandMother-Example

Observation-NoTransfusionProbandMother-Example

Observation-NoBoneMarrowTransplantProbandMother-Example

ServiceRequest-WGSTestOrderForm-TrioTestingProbandMother-Example

Details for Father added to an additional consultand request (sample not collected at time of submission):

Patient-PheobeSmithamFather-Example

RelatedPerson-JamesLawrenceProbandFather-Example

Observation-NonConsanguinousUnionProbandFather-Example

Observation-NoTransfusionProbandFather-Example

Observation-NoBoneMarrowTransplantProbandFather-Example

Observation-IntellectualDisabilityMild-Example

ServiceRequest-WGSTestOrderForm-TrioTestingProbandFather-Example

Details for Family Pedigree Representation

Group-FamilyPedigreeRepresentation-Example

Record of Discussion form resources added to the appropriate requests (YPA and CD forms for Pheobe Smitham and RoD for the Mother, Father's RoD/consent not collected at time of submission):

Consent-RoD-PheobeSmitham-Example

Consent-RoD-PheobeSmithamYoungPersonAssentForm-Example

Consent-RoD-PheobeSmithamMother-Example

QuestionnaireResponse-RoD-PheobeSmithamCDForn-Example

QuestionnaireResponse-RoD-PheobeSmithamYPAForm-Example

QuestionnaireResponse-RoD-PheobeSmithamMother-Example

4. Requester indicates that sample is going to be collected at a later date

Indicated through absence of Specimen resource in message or absence of Specimen.collectedDateTime/Specimen.status=unavailable for appropriate specimen

The lab receives the test request and:

1. Views the completed test order form

Obtained through GET /ServiceRequest or /GET Task requests (using parameters on CapabilityStatements to filter results) for non-routed requests. (Dashboard of available requests)

OR

Obtained through GET /Task request (filtered by GLH owner) for routed requests.

Then

GET /Task by Id and referenced ServiceRequest for view of individual.

2. Indicates awaiting sample/ ROD from father and changes request to awaiting further information

PUT of Task-WGSRareDiseaseTestOrderHold-TrioTestingProband-Example

3. When all samples/ ROD arrives at the lab, test request is triaged and accepted

Receipt of:

Consent-RoD-PheobeSmithamFather-Example (wrapper for RoD)

QuestionnaireResponse-RoD-PheobeSmithamFather-Example (RoD if collected as structured QuestionnaireResponse)

Specimen-PheobeSmithamFather-Example (collected specimen)

ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example (creation of consultand SR to link consent/specimen)

Provenance-WGSTestOrderForm-TrioTestingProbandFather-Example (Provenance to track reason for change to SR)

PUT of Task-WGSRareDiseaseTestOrderAccepted-TrioTestingProband-Example

AND

Task-WGSRareDiseaseTestOrderAccepted-TrioTestingFather-Example

AND

Task-WGSRareDiseaseTestOrderAccepted-TrioTestingMother-Example (for Tasks related to the prepping of the Mother's and Father's samples)

4. Lab forwards test request/ ROD/ samples to GEL/NGIS.

Change of owner on Task to GEL.

TBC: The specific Task triggering the start of the GEL workflow is still under discussion. This may be the ProcessGenomicTestRequest task, after prerequisite RoD and Samples have been added, or may be the set of SamplePrep Tasks (one per Specimen) after prep has been completed by the managing GLH.

5. Requester checks current status of test request

GET /Task(s) with focus ServiceRequest for status of each task (e.g. Sample Sequencing, Interpretation etc.), subsequent call for /AuditEvent(s) with entity.what=Task for history of updates to tasks if needed (e.g. accepted, in-progress, completed)

6. Requester views final report on patient

Task marked as completed: Task-WGSRareDiseaseTestOrderCompleted-TrioTestingProband-Example

DiagnosticReport, referenced from Task: DiagnosticReport-PhoebeSmithGeneticReport-Example