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201601 FHIR Genomics

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FHIR Genomics

Submitting WG/Project/Implementer Group

CG

Justification

FHIR Genomics consists of the Sequence resource and several profiles built on top of existing FHIR resources (DiagnosticReport-genetics profile, DiagnosticOrder-genetics profile, Observation-geneitcs profile). The Sequence resource is a core resource in FHIR Genomics. It is used to represent complex genetics data. FHIR Genomics focuses on clinical genetics data reporting.

Proposed Track Lead

Gil Alterovitz

Expected participants

The number of the participants may be 20-50.

Roles

FHIR Client

Support the sending of the Sequence resource/genetics profiles operations: create, history, read, search and update.

FHIR Server

Support the receiving and processing of the Sequence resource/genetics profiles operations: create, history, read, search and update.

Steps

Scenario 1 Register a new sequence

Action: (FHIR Client) Create a sequence instance to represent genetics data (DNA variant, RNA sequence, structural variant, etc).
Precondition: This sequence instance does not exist in service prior to action.
Success Criteria: Sequence created correctly on server and in the desired format.
Bonus point: New profiles can be built on top of the Sequence resource for complex representation

Example for genetics data representation:

Scenario 2 Search genetics observations from germline analysis

Action: (FHIR Client) Search target observation with patient ID and value for source ("germline")
Precondition: Relevant patient and observations have been created
Success Criteria: A bundle of genetics observations from germline analysis of that patient are returned.
Bonus point: More parameters can be added for searching

Example for corresponding API call and search results

Scenario 3 Clinical and Research Data Warehouses

Action: (FHIR Client) Get all genetic-profile-based observations of patients with the variant c.181T>G
Precondition: Relevant observations have been created
Success Criteria: A bundle of genetics observations, whose extesion 'sequence' referring to sequence instance of variant c.181T>G, are returned.
Bonus point: More parameters can be added for searching

Example for corresponding API call and search results

Scenario 4 Family Member History

Action: (FHIR Client) Get the genetics diagnostic reports of patient's family members.
Precondition: Relevant diagnostic reports have been created
Success Criteria: The genetics diagnostic reports of patient's family members are returned
Bonus point: More parameters can be added for searching

Example for corresponding API call and search results

Scenario 5 Comprehensive Genetics Report

Action: (FHIR Client) Create a comprehensive genetics report for a patient.
Precondition: This diagnostic reports have never been created
Success Criteria: Sequence created correctly on server and in the desired format.
Bonus point: Extensions can be added.

Example for comprehensive report xml codes for comprehensive report


TestScript(s)