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:
| https://zoom.us/j/3176111369 | 317 611 1369 |
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.