201809 Clinical Genomics

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Return to September 2018 Proposals

Clinical Genomics Track

This track will focus on exchanging Genetic Diagnostic Reports in FHIR R4 as described in the Clinical Genomics Reporting IG

For this track, we will be using the balloted STU4 version of FHIR.

Orientation

FHIR Connectathon 19 Track Orientation Slides

Clinical Genomics Reporting IG

Clinical Genomics Track Orientation Recording

Focus of the Connectathon:

DiagnosticReport:

Genetics Diagnostic Report

Findings

Genetic Findings

Interpretations

Genetic Interpretations

Impacts

Genetic Impacts

Sequenced Variants

Sequenced Variants

Zulip Chat

The Zulip Chat will be used to coordinate among participants during the connectathon:

Zulip Chat

Submitting WG/Project/Implementer Group

Justification

After getting Feedback from the first ballot of the Clinical Genomics Implementation Guide in the May 2018 ballot cycle, the balloted IG and profiles should be tested in the Connectathon to get feedback from implementers using it.

Proposed Track Lead

Patrick Werner (patrick.werner@molit.eu)

See Connectathon_Track_Lead_Responsibilities

Expected participants

Kevin P
Bob M
Alex M
Joseph K (?)
Paul Lynch (NLM)
Ye Wang (NLM)
Amnon Shabo (Shvo)
Dora Finkeisen (?)
Patrick Werner (Molit Institut)
Joel Schneider

Roles

  • Genomic Diagnostic Report producer (Lab)
  • Genomic Diagnostic Report consumer(Hospital)

Scenarios

Genetic Diagnostic Report (GDR) as single resources

1. Create a GDR

Examples of paper based Genetic Diagnostic Reports can be found here.
Action: GDR Producer creates a new Genomic Diagnostic Report instance, including all needed referenced Observation Resource Instances like Interpretation, Impact, Described Variant, etc., that is conformant with the Genetics Diagnostic Report profile.
Precondition: none
Success Criteria: GDR passes validation against the Diagnostic Report schema and is identified as valid against the GDR profile by the FHIR profile validation tool or through validation in a FHIR server.

2. Submit GDR

Action: GDR Producer submits Diagnostic Report and referenced Resources to a FHIR Test Server.
Precondition: GDR has been created, GDR Producer knows base URL of the used FHIR Server.
Success Criteria: GDR and referenced Resources are stored on FHIR Server

3. Query GDR

Action: GDR Consumer searches a FHIR Server for a specific GDR using one or more search criteria.
Precondition: GDR and referenced Resources are available on the test server.
Success Criteria: GDR and referenced Resources are returned
Bonus point: Visual Representation of the GDR

Exchange of Genetic Diagnostic Report (GDR) as a document

1. Create a GDR document

Action: GDR Producer creates a new Genomic Diagnostic Report document instance.
Precondition: A validated GDR.
Success Criteria: The GDR document passes validation on a FHIR server.

2. Submit GDR Action: GDR Producer submits a Diagnostic Report document bundles to a FHIR Test Server. Precondition: GDR document has been created, GDR Producer knows base URL of the used FHIR Server. Success Criteria: GDR document is stored on FHIR Server.

Bonus point: POSTing single resources and creating the document bundle on-the-fly using the $document operation.

3. Query GDR

Action: GDR Consumer searches a FHIR Server for a specific GDR document using one or more search criteria.
Precondition: GDR document is available on the test server.
Success Criteria: GDR document is returned.
Bonus point: Visual Representation of the GDR