1. Standard Analyses and Code Sharing Working Group
Project Updates
US CSS
20 March 2017

2. SDA: Script Discovery and Acquisition
Project Description
Discover, acquire and review scripts to be stored in the repository with adequate metadata to describe the scripts
Project Leads
Rebeka Revis
Alfredo Rojas

3. P01 - SDA: Script Discovery and Acquisition
Project Accomplishments
JumpStart scripts have been contributed
A couple in 2015, additional scripts early 2016, modified scripts early 2017
First draft of scripts have been tested, a couple modified scripts have been tested
White paper with JumpStart screen shots – hope to finalize in March 2017
Non-clinical scripts, scripts related to data handling, and an interactive safety review have also been contributed

4. SDA: Script Discovery and Acquisition
Adverse Event Severity (AE_Severity)
Accenture: Alfredo Rojas
Novo Nordisk: Lina Ulkjær
Adverse Event Toxicity (AE_Toxicity)
Demographics (DemographicsGeneral)
Disposition (DispositionGeneral)
Exposure (ExposureGeneral)
Liver Labs (LiverLabsGeneral)
MedDRA at a Glance (MedDRA_at_a_Glance – ae_meddra_w_flag_generation.sas)
The list above gives the script and the script tester(s).

5. SDA: Script Discovery and Acquisition
Project Next Steps
Continue testing modified JumpStart Scripts (need additional volunteers)
Will continue to monitor for additional scripts that may make sense for the PhUSE Repository
We also need a JumpStart representative to help us respond to reviewer comments.

6. P02 - RCD: Repository Content and Delivery
Project Description
Develop and enhance scripts under a defined qualification process to ensure the usability and quality of the standard scripts
Project Leads
Gustav Bernard
Andrew Miskell

7. RCD: Repository Content and Delivery
Team Distributed in 2 Target Teams
Target Team 1: Nancy Brucken
Target Team 2: Alex Ford
Each Team worked on Separate Target Deliveries / Outputs

8. RCD: Repository Content and Delivery
Project Accomplishments
GitHub script repository
Project Programming Guidelines
Streamlined Qualification Process
Central Tendency package Qualification Completed
6 Recommended displays in CT White Paper

9. RCD: Repository Content and Delivery
Project Next Steps
Central Tendency Shifts
Scripts for SAS only
Scripts less Macro dependent (Stand alone program for easy download and use)
2017 FDA Representative: Dr. Qing Zhou

10. P03 - RGI: Repository Governance and Infrastructure
Project Description:
Establish the basic structure and management of the repository.
Define and enforce existence of required metadata for scripts
Manage users and projects in the repository
Project Leads:
Mike Carniello
Hanming Tu

11. RGI: Repository Governance and Infrastructure
Project Accomplishments
MIT license chosen:
Qualification guidelines developed:
User-friendly front end developed:
Repository has been updated to have a place to store scripts developed by other groups
More people have joined the development team (28 now):

12. RGI: Scripts Contributed
Scripts contributed by other groups
FDA:
Non-clinical:
Data Handle:
Spotfire Templates:

13. RGI: Scripts Developed
Scripts developed by volunteers
6 Scriptathons (plus additional work by project members) resulting in several scripts at various stages
Focused on creating scripts associated with the displays in the white papers, starting with ADaM data
The specifications for the scripts include assumptions and required ADaM variables
Starting with CDISC pilot data
Scripts developed based on white paper
Central Tendency package Qualification Completed: 6 Recommended displays in CT White Paper

14. RGI: Repository Governance and Infrastructure
Project Next Steps
Continue maintaining repository structure
Continue managing users and accesses to the repository
Define how to use YML for script metadata
Define and explore script test environment

15. P07 - CPE: Communication, Promotion, and Education
Project Description
Conceptualize Efficient Ways to Communicate Working Group Progress and Results
Project Leads
Jared Slain
Wendy Dobson

16. CPE: Communication, Promotion, and Education
Project Accomplishments
Presentations:
List of past/present/future working group member presentations on PhUSE Wiki
Presentations
JumpStart scripts – 2016 PhUSE Annual Conference
GitHub User Guide – 2017 CSS

17. CPE: Communication, Promotion, and Education
Project Accomplishments cont’d
Compiled ongoing list of events for promoting WG
Use of social media to advertise White Papers
As co-lead, Wendy provides streamlined integration with PhUSE Office

18. CPE: Communication, Promotion, and Education
Project Next Steps
Keep project page on PhUSE Wiki updated
Find people already going to events to present/promote working group
Work with White Papers project to enhance White Paper visibility
Training Material

19. P08 - ADW: Analysis and Display White Papers
Project Description
This project includes the development of white papers that provide recommended Tables, Figures, and Listings for clinical trial study reports and submission documents. The intent is to begin the process of developing industry standards with respect to analysis and reporting for measurements that are common across clinical trials and across therapeutic areas. Script developers could then create scripts consistent with the recommendations for all to use, improving efficiency and safety signal detection.
Project Lead – Mary Nilsson

20. ADW: Analysis and Display White Papers
How to find final white papers: Go to Click on Working Groups, Click on CS Deliverables Catalog
Project Accomplishments
6 White Papers finalized
Vital Signs, ECGs, Labs - Central Tendency
Finalized in October 2013, Lead – Mary Nilsson
Non-Compartmental Pharmacokinetics
Finalized in March 2014, Lead - Francois Vandenhende
Demographics, Disposition, and Medications
Finalized October 2014, Lead – Simin Baygani
Vital Signs, ECGs, Labs – Outliers and Shifts
Finalized in September 2015, Lead – Wei Wang
QT/QTc Studies
Finalized in March 2016, Lead – Christos Stylianou
Adverse Events
Finalized February 2017, Lead – Mary Nilsson, Nhi Beasley, Sheryl Treichel

21. ADW: Analysis and Display White Papers
Project Next Steps
AE White Paper follow-up tasks
Gender- and Pediatric-specific MedDRA lists
Process for Grouping MedDRA terms
Work on 4 new white papers
Hepatotoxicity
Questionnaire data
Treatment-emergent definitions
Adverse events of special interest
Work on version 2 of a couple white papers
Demographics/Dispostion/Medications
Labs/Vitals/ECGs

22. Analysis and Display White Papers Project Team
Version 1
Version 2
Public
Review
Published
Public Review
Vital Signs, Labs, ECG –
Central Tendency
Oct 2013
Q4 2017
Non-Compartmental PK
March 2014
Demographics, Disposition, Medications
Oct 2014
Q3 2017
Outliers / Shifts
Sept 2015
QT/QTc Studies
March 2016
Adverse Events
Feb 2017
Treatment-Emergent Definitions
Hepatotoxicity
Questionnaires
Events of Special Interest

23. ADW: Analysis and Display White Papers
Project Next Steps (continued)
Communication and Education
Will network with the CPE project team
Will likely focus on “Core” package (demographics, disposition, medications, AEs, labs, vitals, ECGs)
Will likely include multiple approaches (live educational and informational sessions, webinars, video clips, etc.)
Please help – anyone attending a conference can cover a roundtable or poster – we will help!

24. P09 - TDF: Test Data Factory
Project Background:
Several PhUSE projects develop scripts/concepts that need to be tested with trial data sets
Use of CDISC pilot datasets and/or data sets from team members for testing isn’t sufficient in many cases
Project Approach and Objective:
Determine test dataset requirements
Short versus long term approach:
Create test data sets from existing study data
Implement scripts that create ‘simulated’ SDTM and/or ADaM test data sets
Publish datasets, and if possible, user-configurable scripts
Project co-lead: Peter Schaefer

25. TDF: Test Data Factory Project Accomplishments
Project team has been established
We still can use additional team members
Decided to update existing CDISC pilot data to be consistent with current SDTM/ADaM standards with two objectives
Produce useful results quickly
Establish knowledge base for issues around ‘simulating’ test data sets
Update of SDTM domains in progress
Some domains are done (trial design, DM, …)
See poster PP16 for more information

26. TDF: Test Data Factory Project Next Steps
Continue to recruit project members
Short term:
Complete update of CDISC Pilot data sets and publish
Mid term:
Create Proof of Concept for ‘simulated’ test data sets