R pilots

Pilot principles:

Provide open examples of submitting R-based clinical trial data/analysis packages to FDA.

• All pilots will be submitted from R consortium (non-profit identity) to FDA. Simulated data will be used.
• All data, codes and documents will be fully available to public.
• FDA Staff will be engaged to reproduce analysis results.
• Submitter and FDA Staff will provide feedback on current process/system
• Contributions from multiple companies/organizations are preferred. Avoid bias to any company/organization specific tools.

Pilot 1 - common analyses

Goal: Example R based submission contains common analyses, submission through the current FDA e-submission system and process.

Key evaluation aspects:

• For Submitter
  • Submission of proprietary R packages
  • Preparation of R-based submission materials
• For FDA Staff
  • Reproduce analysis results by reconstructing submitted proprietary packages / retrieving open source packages

Data and analysis scope:

• 4 TLFs
• Simulated data from CDISC Pilot

Success Criteria:

• Submitter:
  • Successfully submit via eCTD portal
• FDA Reviewer:
  • Reproduce analysis results

Timeline: - Submitted 2021 Nov (v0.1.0) - FDA first response 2021 Nov - Resubmission 2022 Feb (v0.1.0)

Links:

R Submission Pilot 1 Development Repo

R Submission Pilot 1 eCTD Submission Package to FDA

Additional Activities - explore pilot submissions to other HAs (Japan, China)

Key team members:

Developer team:

Ning Leng, Heng Wang (Roche)
Mike Stakehouse, Eli Miller (Atorus)
Yilong Zhang, Peikun Wu (Merck)

Esub team:
Beverly Chin (Roche)
Tim Powell (Biogen)

FDA Staff:
Paul Schuette
Hye Soo Cho

Pilot 2 - shiny submission

Goal: Example R based submission contains a shiny app, submission through the current FDA e-submission system and process

Key evaluation aspects:

• For Submitter
  • Submission of an shiny app through the eCTD portal
  • The shiny codes will be provided as a proprietary R package
• For FDA Reviewer
  • Reproduce analysis results by deploying the shiny app on a FDA laptop/server

Timeline: 2022 H1

Data and analysis scope:

• a shiny app that displays the 4 TLFs submitted in pilot 1, with basic data set filtering functionalities.
• Simulated data from CDISC Pilot (the same data set as in pilot 1)

Links:

R Submission Pilot 2 Development Repo

R Submission Pilot 2 eCTD Submission Package to FDA

Key team members: Developer team:

Ning Leng, Heng Wang (Roche)
Mike Stakehouse, Eli Miller (Atorus)
Yilong Zhang, Gregery Chen (Merck)
Eric Nantz (Eli Lilly)

FDA Staff:
Paul Schuette
Hye Soo Cho

Pilot 3 - alternative formats

Goal: Example R based submission exploring alternative options than current FDA e-submission system and process (e.g. container) Timeline: TBD

Developer team:

Eric Nantz (Eli Lilly)