Title: Screen Shots of the Displays Created by JumpStart Programs / Working Group: Standard Analyses and Code Sharing
PhUSE
PhUSE Computational Science Standard Analyses and Code Sharing Working Group
Script Discovery and Acquisition Project Team
Screen Shots of the Displays Created by JumpStart Programs
Table of Contents
1. Disclaimer 3
2. Notice of Current Edition 3
3. Additions and/or Revisions 3
4. Purpose 3
5. Acknowledgements 4
6. Project Leader Contact Information 4
7. References 4
8. Appendices 5
8.1. AE Severity 5
8.2. AE Toxicity 13
8.3. Demographics 18
8.4. Disposition 23
8.5. Exposure 26
8.6. Liver 31
1. Disclaimer
The opinions expressed in this document are those of the authors and do not necessarily represent the opinions of the Pharmaceuticals User Software Exchange (PhUSE), members' respective companies or organizations, or regulatory authorities. The content in this document should not be interpreted as a data standard and/or information required by regulatory authorities.
2. Notice of Current Edition
This edition of the “Screen Shots of the Displays Created by JumpStart Programs” white paper is the first edition.
3. Additions and/or Revisions
Date / Author / Version / Changes2017-Mar-17 / See Section 5 / v1.0 / First edition
4. Purpose
The purpose of this document is to show the displays that are created when the FDA utilizes their JumpStart service when receiving clinical trial data as part of a submission. As noted on Food and Drug Administration’s (FDA’s) web site [1], JumpStart runs a series of drug clinical trial data analyses early in the review process to assess data composition, quality, analyses options, and tools for the analyses, so reviewers have a better understanding of the data and have the information to conduct an effective evaluation of the drug submission. JumpStart provides these data findings to the reviewers shortly after the receipt of a new submission, giving reviewers time to clarify issues or make requests of the organizations developing the drug before proceeding in the review process. JumpStart also provides data analyses that highlight areas of concern and may warrant further attention. For additional information on JumpStart including what it is, its benefits, and how it works, visit the FDA’s web site [1].
The displays provided here are not necessarily consistent with regulatory guidance documents or white papers created by the PhUSE Analysis and Display White Papers (ADW) Project Team. We do not recommend that sponsors create these tables and figures instead of those already in a sponsor’s standards library or those that are recommended by the PhUSE ADW project team. Instead, these displays inform sponsors of what the FDA will likely see early in their review process. Updates or modifications to a sponsor’s standards may be warranted if conceptual gaps are identified. However, sponsors may want to run the JumpStart scripts to ensure the FDA will be able to run them without errors. The FDA shared their JumpStart scripts with the PhUSE Script Repository Discovery and Acquisition Project Team and the scripts have been uploaded to the PhUSE Script Repository in GitHub [2].
If interested in ensuring the FDA will be able to run the JumpStart scripts without errors or in duplicating the displays, sponsors can start with and access the codes provided in the PhUSE Script Repository in GitHub by following these links:
· Index of all scripts: https://github.com/phuse-org/phuse-scripts/wiki/Simple-Index
· Index of FDA JumpStart Scripts: https://github.com/phuse-org/phuse-scripts/wiki/JumpStart-Scripts.
· Once a script is tested, it will be in the tested/SAS folder
5. Acknowledgements
The primary contributors include Rebeka Revis, Hamning Tu, Mary Nilsson, and Ted Peterson. Thank you to Casie Polanco for editorial support. Thank you to all the original authors of the JumpStart scripts and those involved with updates to the scripts over time.
6. Project Leader Contact Information
Rebeka Revis
Eli Lilly & Company
Indianapolis, IN 46285
Work Phone: (317) 503-6480
E-mail:
7. References
1. JumpStarting Drug Review. Food and Drug Administration web site. Available at: https://www.fda.gov/Drugs/ResourcesForYou/Consumers/ucm397921.htm. Accessed 13 Feb 2017.
2. Slain J, Tu H. CS07: Get a Jump Start on Clinical Data Analysis and Visualization with Standard Scripts. PhUSE Wiki. Available at: http://www.phusewiki.org/docs/Conference%202016%20CS%20Paper/CS07.pdf. Accessed 13 Feb 2017.
Script Discovery and Acquisition Project Team – Version 1.0 – 2017-Mar-17
21
/ Project: Script Discovery and Acquisition Project TeamTitle: Screen Shots of the Displays Created by JumpStart Programs / Working Group: Standard Analyses and Code Sharing
8. Appendices
8.1. AE Severity
Analysis 1: Adverse Events by Arm Greater than 2%
Analysis 2: Serious Adverse Events by Arm
Analysis 3: Adverse Events by Severity and Arm
Analysis 4: Serious Adverse Events by Severity and Arm
Script Discovery and Acquisition Project Team – Version 1.0 – 2017-Mar-17
21
/ Project: Script Discovery and Acquisition Project TeamTitle: Screen Shots of the Displays Created by JumpStart Programs / Working Group: Standard Analyses and Code Sharing
Analysis 5.1: Relative Risk
Analysis 5.2: Relative Risk and 95% Interval Analysis
Analysis 6.1: Odds Ratio
Analysis 6.2: Odds Ratio and 95% Interval Analysis
8.2. AE Toxicity
Analysis 1: Toxicity Grade Summary
Script Discovery and Acquisition Project Team – Version 1.0 – 2017-Mar-17
21
/ Project: Script Discovery and Acquisition Project TeamTitle: Screen Shots of the Displays Created by JumpStart Programs / Working Group: Standard Analyses and Code Sharing
Analysis 2: Preferred Term Analysis by Toxicity Grade (V1)
Script Discovery and Acquisition Project Team – Version 1.0 – 2017-Mar-17
21
/ Project: Script Discovery and Acquisition Project TeamTitle: Screen Shots of the Displays Created by JumpStart Programs / Working Group: Standard Analyses and Code Sharing
Analysis 3: Preferred Term Analysis by Toxicity Grade (V2)
Script Discovery and Acquisition Project Team – Version 1.0 – 2017-Mar-17
21
/ Project: Script Discovery and Acquisition Project TeamTitle: Screen Shots of the Displays Created by JumpStart Programs / Working Group: Standard Analyses and Code Sharing
Analysis 4: Two-Term MedDRA Analysis (V1)
Analysis 5: Two-Term MedDRA Analysis
Script Discovery and Acquisition Project Team – Version 1.0 – 2017-Mar-17
21
/ Project: Script Discovery and Acquisition Project TeamTitle: Screen Shots of the Displays Created by JumpStart Programs / Working Group: Standard Analyses and Code Sharing
8.3. Demographics
Analysis 1: Overview
Analysis 2: Age Groups
Analysis 3: Age Groups by Disposition
Analysis 4.1: Age Statistics - Table
Analysis 4.2: Age Statistics - Figure
Script Discovery and Acquisition Project Team – Version 1.0 – 2017-Mar-17
21
/ Project: Script Discovery and Acquisition Project TeamTitle: Screen Shots of the Displays Created by JumpStart Programs / Working Group: Standard Analyses and Code Sharing
Analysis 5: Country and Site ID
Script Discovery and Acquisition Project Team – Version 1.0 – 2017-Mar-17
21
/ Project: Script Discovery and Acquisition Project TeamTitle: Screen Shots of the Displays Created by JumpStart Programs / Working Group: Standard Analyses and Code Sharing
8.4. Disposition
Analysis 1: Disposition Events by Arm for All Subjects
Analysis 2: Disposition Events by Arm for Exposed Subjects
Analysis 3: Time to Disposition Event by Arm for All Subjects
Analysis 4: Time to Disposition Event by Arm for Exposed Subjects
8.5. Exposure
Analysis 1: Total Number of Days of Drug
Analysis 2: Cumulative Dose
Analysis 3: Dose Descriptive Statistics and Boxplot of Doses by Arm
Script Discovery and Acquisition Project Team – Version 1.0 – 2017-Mar-17
21
/ Project: Script Discovery and Acquisition Project TeamTitle: Screen Shots of the Displays Created by JumpStart Programs / Working Group: Standard Analyses and Code Sharing
Analysis 4: Count of Subjects by Treatment Arm and Actual Treatment
Analysis 5: Dose Changes during the Study
Script Discovery and Acquisition Project Team – Version 1.0 – 2017-Mar-17
21
/ Project: Script Discovery and Acquisition Project TeamTitle: Screen Shots of the Displays Created by JumpStart Programs / Working Group: Standard Analyses and Code Sharing
8.6. Liver
Analysis 1: Liver Lab Tests Greater Than Upper Limit of Normal
Analysis 2.1: Combinations for Possible Hy’s Law Cases at the Same Visit
Analysis 2.2: Combinations for Possible Hy’s Law Cases at Any Time during the Study
Analysis 2.3: Combinations for Possible Hy’s Law Cases Patients at Any Time during the Study
Analysis 3: Baseline Lab Tests – Maximum vs Baseline
Analysis 4: Maximum AST/ALT vs Maximum TB Lab Test Results per Subject Charts
Analysis 5: Maximum Lab Test Results per Subject by Study Day
Script Discovery and Acquisition Project Team – Version 1.0 – 2017-Mar-17
21