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Track touchpoint meetings:

Thursday 9:30 AM ET - Genomics kickoff

Thursday 6:00 PM ET - Touchbase

Friday 9:30 AM ET - Touchbase

Friday 6:30 PM ET - Connectathon wrapup session

Track specific Zoom:

Submitting WG/Project/Implementer Group

Clinical Genomics

Justification and Objectives

What’s the purpose of hosting this connectathon track? What do you hope to achieve?

We plan to continue validating our recent STU1 release, and ensure upcoming changes for STU2 support appropriate use cases.

This track will use what version of FHIR.

FHIR 4.0.1

Genomics Reporting STU1

Genomics Reporting Current Build

Clinical input requested (if any)

Validation of use cases

Related tracks 


Track Leads

Jamie Jones: james.jones.bch@gmail.com

Patrick Werner: pa.f.werner@gmail.com

Kevin Power: kpower@cerner.com


Expected participants

Bob Dolin
Alex Mankovich
Bret Heale
Arthur Hermann



Track Orientation


System Roles


Oncology Testing Lab

Producing tumor-normal report containing genomics report, multiple variants, diagnostic, and therapeutic implications

Inherited Disease/WES Testing Lab

Producing WES report containing genomics report, multiple variants, diagnostic, and therapeutic implications

eMERGE Testing Lab

Producing eMERGE style reports

Genomics Data Archive System

Produce Genomics Reporting IG compliant responses based on VCF or other 'raw' underlying genomic data and demonstrate use in a CDS pipeline


Scenarios

Scenario 1: Report Logging

Action: Testing Lab (client) creates a FHIR genomics report adherent to either Genomics Reporting STU1.0 or the current CI build and sends it to a FHIR server's endpoint.

Precondition: Report is not present on the target server.

Success Criteria: Report is queryable on the FHIR endpoint.

Bonus point: Feedback on report structure, query results, and validation errors for different use cases. 


Scenario 2: ACMG Screening

Action: Client makes api calls to a Genomic data server implementing the draft $find-subject-variants in an attempt to confirm presence of ACMG secondary findings. See for example https://www.ncbi.nlm.nih.gov/clinvar/docs/acmg/.

Precondition: Genomic data server is populated with appropriate VCF and/or FHIR Genomics observations.

Success Criteria: Client is able to identify ACMG secondary findings among the genomic data.

Bonus point: Create a mock lab report including the secondary findings and complete scenario 1 with it.


TestScript(s)

WIP, java validator until then.


Security and Privacy Considerations

All data used in this track is assumed to be fully de-identified or consented for completely open use.

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