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Quantitative
Evaluation of
Safety in Drug
Development
Design, Analysis
and Reporting

Edited by
Qi Jiang
H. Amy Xia
 Quantitative
Evaluation of
Safety in Drug
Development
Design, Analysis
and Reporting
Editor-in-Chief
Shein-Chung Chow, Ph.D., Professor, Department of Biostatistics and Bioinformatics,
Duke University School of Medicine, Durham, North Carolina

Series Editors
Byron Jones, Biometrical Fellow, Statistical Methodology, Integrated Information Sciences,
Novartis Pharma AG, Basel, Switzerland
Jen-pei Liu, Professor, Division of Biometry, Department of Agronomy,
National Taiwan University, Taipei, Taiwan
Karl E. Peace, Georgia Cancer Coalition, Distinguished Cancer Scholar, Senior Research Scientist
and Professor of Biostatistics, Jiann-Ping Hsu College of Public Health,
Georgia Southern University, Statesboro, Georgia
Bruce W. Turnbull, Professor, School of Operations Research and Industrial Engineering,
Cornell University, Ithaca, New York

Published Titles
Adaptive Design Methods in Bayesian Methods in Health Economics
Clinical Trials, Second Edition Gianluca Baio
Shein-Chung Chow and Mark Chang Bayesian Missing Data Problems: EM,
Adaptive Design Theory and Data Augmentation and Noniterative
Implementation Using SAS and R, Computation
Second Edition Ming T. Tan, Guo-Liang Tian,
Mark Chang and Kai Wang Ng
Advanced Bayesian Methods for Medical Bayesian Modeling in Bioinformatics
Test Accuracy Dipak K. Dey, Samiran Ghosh,
Lyle D. Broemeling and Bani K. Mallick
Advances in Clinical Trial Biostatistics Benefit-Risk Assessment in
Nancy L. Geller Pharmaceutical Research and
Applied Meta-Analysis with R Development
Ding-Geng (Din) Chen and Karl E. Peace Andreas Sashegyi, James Felli, and
Rebecca Noel
Basic Statistics and Pharmaceutical
Statistical Applications, Second Edition Biosimilars: Design and Analysis of
James E. De Muth Follow-on Biologics
Shein-Chung Chow
Bayesian Adaptive Methods for
Clinical Trials Biostatistics: A Computing Approach
Scott M. Berry, Bradley P. Carlin, Stewart J. Anderson
J. Jack Lee, and Peter Muller Causal Analysis in Biomedicine and
Bayesian Analysis Made Simple: An Excel Epidemiology: Based on Minimal
GUI for WinBUGS Sufficient Causation
Phil Woodward Mikel Aickin

Bayesian Methods for Measures of Clinical and Statistical Considerations

Agreement in Personalized Medicine
Lyle D. Broemeling Claudio Carini, Sandeep Menon,
and Mark Chang
Bayesian Methods in Epidemiology
Lyle D. Broemeling Clinical Trial Data Analysis using R
Ding-Geng (Din) Chen and Karl E. Peace
Clinical Trial Methodology Dose Finding by the Continual
Karl E. Peace and Ding-Geng (Din) Chen Reassessment Method
Computational Methods in Biomedical Ying Kuen Cheung
Research Elementary Bayesian Biostatistics
Ravindra Khattree and Dayanand N. Naik Lemuel A. Moyé
Computational Pharmacokinetics Frailty Models in Survival Analysis
Anders Källén Andreas Wienke
Confidence Intervals for Proportions and Generalized Linear Models: A Bayesian
Related Measures of Effect Size Perspective
Robert G. Newcombe Dipak K. Dey, Sujit K. Ghosh,
Controversial Statistical Issues in and Bani K. Mallick
Clinical Trials Handbook of Regression and Modeling:
Shein-Chung Chow Applications for the Clinical and
Data and Safety Monitoring Committees Pharmaceutical Industries
in Clinical Trials Daryl S. Paulson
Jay Herson Inference Principles for Biostaticians
Design and Analysis of Animal Studies in Ian C. Marschner
Pharmaceutical Development Interval-Censored Time-to-Event Data:
Shein-Chung Chow and Jen-pei Liu Methods and Applications
Design and Analysis of Bioavailability and Ding-Geng (Din) Chen, Jianguo Sun,
Bioequivalence Studies, Third Edition and Karl E. Peace
Shein-Chung Chow and Jen-pei Liu Joint Models for Longitudinal and Time-
Design and Analysis of Bridging Studies to-Event Data: With Applications in R
Jen-pei Liu, Shein-Chung Chow, Dimitris Rizopoulos
and Chin-Fu Hsiao Measures of Interobserver Agreement
Design and Analysis of Clinical Trials with and Reliability, Second Edition
Time-to-Event Endpoints Mohamed M. Shoukri
Karl E. Peace Medical Biostatistics, Third Edition
Design and Analysis of Non-Inferiority A. Indrayan
Trials Meta-Analysis in Medicine and Health
Mark D. Rothmann, Brian L. Wiens, Policy
and Ivan S. F. Chan Dalene Stangl and Donald A. Berry
Difference Equations with Public Health Mixed Effects Models for the Population
Applications Approach: Models, Tasks, Methods and
Lemuel A. Moyé and Asha Seth Kapadia Tools
DNA Methylation Microarrays: Marc Lavielle
Experimental Design and Statistical Monte Carlo Simulation for the
Analysis Pharmaceutical Industry: Concepts,
Sun-Chong Wang and Arturas Petronis Algorithms, and Case Studies
DNA Microarrays and Related Genomics Mark Chang
Techniques: Design, Analysis, and Multiple Testing Problems in
Interpretation of Experiments Pharmaceutical Statistics
David B. Allison, Grier P. Page, Alex Dmitrienko, Ajit C. Tamhane,
T. Mark Beasley, and Jode W. Edwards and Frank Bretz
Noninferiority Testing in Clinical Trials: Statistical Analysis of Human Growth
Issues and Challenges and Development
Tie-Hua Ng Yin Bun Cheung
Optimal Design for Nonlinear Response Statistical Design and Analysis of
Models Stability Studies
Valerii V. Fedorov and Sergei L. Leonov Shein-Chung Chow
Patient-Reported Outcomes: Statistical Evaluation of Diagnostic
Measurement, Implementation and Performance: Topics in ROC Analysis
Interpretation Kelly H. Zou, Aiyi Liu, Andriy Bandos,
Joseph C. Cappelleri, Kelly H. Zou, Lucila Ohno-Machado, and Howard Rockette
Andrew G. Bushmakin, Jose Ma. J. Alvir, Statistical Methods for Clinical Trials
Demissie Alemayehu, and Tara Symonds Mark X. Norleans
Quantitative Evaluation of Safety in Drug Statistical Methods in Drug Combination
Development: Design, Analysis and Studies
Reporting Wei Zhao and Harry Yang
Qi Jiang and H. Amy Xia
Statistics in Drug Research:
Randomized Clinical Trials of Methodologies and Recent
Nonpharmacological Treatments Developments
Isabelle Boutron, Philippe Ravaud, and Shein-Chung Chow and Jun Shao
David Moher
Statistics in the Pharmaceutical Industry,
Randomized Phase II Cancer Clinical Third Edition
Trials Ralph Buncher and Jia-Yeong Tsay
Sin-Ho Jung
Survival Analysis in Medicine and
Sample Size Calculations for Clustered Genetics
and Longitudinal Outcomes in Clinical Jialiang Li and Shuangge Ma
Research
Theory of Drug Development
Chul Ahn, Moonseong Heo, and
Eric B. Holmgren
Song Zhang
Translational Medicine: Strategies and
Sample Size Calculations in Clinical
Statistical Methods
Research, Second Edition
Dennis Cosmatos and Shein-Chung Chow
Shein-Chung Chow, Jun Shao
and Hansheng Wang
 Quantitative
Evaluation of
Safety in Drug
Development
Design, Analysis
and Reporting

Edited by

Qi Jiang
Amgen Inc
Thousand Oaks, California, USA

H. Amy Xia
Amgen Inc
Thousand Oaks, California, USA
CRC Press
Taylor & Francis Group
6000 Broken Sound Parkway NW, Suite 300
Boca Raton, FL 33487-2742
© 2015 by Taylor & Francis Group, LLC
CRC Press is an imprint of Taylor & Francis Group, an Informa business

No claim to original U.S. Government works

Version Date: 20141017

International Standard Book Number-13: 978-1-4665-5547-1 (eBook - PDF)

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Contents

Preface.......................................................................................................................ix
Editors.......................................................................................................................xi
Contributors.......................................................................................................... xiii

Section I Study Design

1. Incorporating Quantitative Safety Evaluation into Risk

Management..................................................................................................... 3
Jürgen Kübler

2. Bayesian Meta-Experimental Design for Evaluating

Cardiovascular Risk...................................................................................... 13
Joseph G. Ibrahim, Ming-Hui Chen, H. Amy Xia, Thomas Liu,
and Violeta Hennessey

3. Non-Inferiority Study Design and Analysis for Safety Endpoints........ 39

Steven Snapinn and Qi Jiang

Section II Safety Monitoring

4. Program Safety Analysis Plan: An Implementation Guide................. 55

Brenda Crowe, H. Amy Xia, Mary Nilsson, Seta Shahin, Wei Wang,
and Qi Jiang

5. Why a DMC Safety Report Differs from a Safety Section

Written at the End of the Trial.................................................................... 69
Mark Schactman and Janet Wittes

6. Safety Surveillance and Signal Detection Process................................. 93

Atsuko Shibata and José M. Vega

vii
viii Contents

Section III Evaluation/Analysis

7. Bayesian Adaptive Trials for Drug Safety............................................. 109

Jason T. Connor

8. Observational Safety Study Design, Analysis, and Reporting......... 125

Hong Qiu, Jesse A. Berlin, and Paul E. Stang

9. Emerging Role of Observational Health-Care Data

in Pharmacovigilance................................................................................. 141
Patrick Ryan, David Madigan, and Martijn Schuemie

10. Roadmap for Causal Inference in Safety Analysis.............................. 173

Jordan C. Brooks, Alan S. Go, Daniel E. Singer, and Mark J. van der Laan

11. Safety Graphics............................................................................................ 195

Susan P. Duke, Qi Jiang, Liping Huang, Mary Banach, and Max Cherny

12. Bayesian Network Meta-Analysis for Safety Evaluation....................223

Bradley P. Carlin and Hwanhee Hong

13. Regulatory Issues in Meta-Analysis of Safety Data............................ 237

Aloka G. Chakravarty and Mark Levenson

14. Bayesian Applications for Drug Safety Evaluation.............................. 251

H. Amy Xia and Karen L. Price

15. Risk-Benefit Assessment Approaches..................................................... 267

Chunlei Ke, Qi Jiang, and Steven Snapinn

16. Detecting Safety Signals in Subgroups.................................................. 289

Christy Chuang-Stein, Yoichi Ii, Norisuke Kawai, Osamu Komiyama,
and Kazuhiko Kuribayashi

17. Overview of Safety Evaluation and Quantitative Approaches

during Preclinical and Early Phases of Drug Development.............. 321
John Sullivan and Hisham Hamadeh
Preface

Drug safety has always been important, but it has undergone increased scru-
tiny in recent years. This book is about quantitative evaluation of the safety
of biopharmaceutical products. The book is meant to be comprehensive, cov-
ering design, monitoring, analysis, and reporting issues for both clinical tri-
als and observational studies. In addition, since statistical methods for drug
safety assessment are still evolving and new methods are under development,
the book will cover developments in state-of-the-art methods for drug safety
assessment. We hope our book will bring the most advanced knowledge and
statistical methodology to the statistical, clinical, and safety community; share
best practices; and stimulate further research and methodology development
in the drug safety area.
The book presents key challenges that impact regulatory agencies, indus-
try, and academia. It elaborates on Bayesian methods, presents approaches to
creating effective safety graphics, and includes consideration for risk-benefit
evaluation. The book is mainly for professionals with a quantitative back-
ground in fields such as statistics or epidemiology working in pharmaceuti-
cal, biotechnology, and device industries; regulatory agencies that govern
these industries; and academic departments involved in activities related to
clinical trials or observational studies in biopharmaceutical product devel-
opment. The book is mainly suitable for research and could also be used as
supplementary material for teaching; for example, for courses on pharma-
ceutical science, biostatistics, applied statistics, statistical computing, clinical
trials, causal inference, and observational studies.
The chapters discuss quantitative approaches to safety evaluation and risk
management in drug development. They cover broad topics such as study
design, safety monitoring, and data evaluation/analysis. First, study design
includes the Bayesian meta-experimental design for evaluating cardiovas-
cular risk, non-inferiority study design and analysis for safety endpoints,
and the program safety analysis plan. Second, safety monitoring is critical,
and on this topic the book includes chapters on why a DMC safety report
differs from a safety report written at the end of the trial, safety surveillance
and signal detection processes, and Bayesian adaptive trials for drug safety.
Finally, the book covers evaluation/analysis topics such as observational
safety study design, analysis, and reporting; the observational medical out-
comes partnership (OMOP); a roadmap for causal inference in safety analy-
sis; safety graphics; Bayesian network meta-analysis for safety evaluation;
regulatory issues in meta-analysis of safety data; Bayesian applications for
drug safety evaluation; risk-benefit assessment approaches; detecting safety
signals in subgroups, and an overview of safety evaluation and quantitative
approaches during preclinical and early phases of drug development.

ix
x Preface

As editors of this book, we are pleased to see that such broad and criti-
cal safety topics have been addressed by well-established and experienced
authors. We trust you will enjoy reading them and find them informative
and useful in your drug safety evaluation as much as we do.
We are very grateful for our family members’ tremendous support and
patience during the completion of the book. We also wish to express our
great appreciation for the terrific support received from David Grubbs,
Laurie Schlags, and the production team at Taylor & Francis Group, LLC.

Qi Jiang, PhD
H. Amy Xia, PhD
Editors

Qi Jiang, PhD, is an executive director of Global Biostatistical Science at

Amgen Inc., Thousand Oaks, California. In this role she is biostatistical
therapeutic area head for bone-related therapies (including indications in
osteoporosis and oncology), is head of the safety biostatistics department,
and provides oversight to Amgen’s biostatistical efforts in Asia. Before join-
ing Amgen she worked at the Harvard School of Public Health, Merck, and
Novartis. She has over 18 years of clinical trial experience in early and late
clinical development phases across a broad spectrum of therapeutic areas
and has authored numerous publications on method development, study
design, and data analysis and reporting.
Dr. Jiang is a co-lead of American Statistical Association Biopharmaceutical
Section Safety Working Group and the Quantitative Sciences in the
Pharmaceutical Industry (QSPI) Benefit-Risk working group and a member of
many initiatives including the Pharmaceutical Research and Manufacturers
of America (PhRMA) Limited Duration Key Issue Team on Benefit-Risk
Harmonization, the Drug Information Association (DIA) Next Steps Working
Group (NSWG) on benefit-risk efforts, and a Clinical Trials Transformation
Initiative (CTTI) team working on the implementation of the FDA (Food and
Drug Administration) IND (Investigational New Drug) safety rule. Dr. Jiang
is an associate editor of the journal Statistics in Biopharmaceutical Research
(SBR), a referee for many other statistical journals and a coeditor for special
issues of two statistical journals on safety and benefit-risk. She is a fellow of
the American Statistical Association. In 2013, Dr. Jiang received a Healthcare
Businesswomen’s Association (HBA) Rising Star award. Her research inter-
ests include drug safety monitoring and analyses, benefit-risk assessment,
clinical meaningfulness, dichotomization, meta-analyses, network meta-
analysis, adaptive design, and noninferiority study design and analyses.

H. Amy Xia, PhD, is executive director in Global Biostatistical Science at

Amgen Inc., Thousand Oaks, California. Dr. Xia has worked on designing,
executing, and reporting clinical trials as well as observational studies for
developing pharmaceutical and medical device products in a wide range of
different disease areas in the past 18 years. Her research interests include
safety biostatistics, signal detection, Bayesian design, monitoring and analy-
sis of clinical trials, meta-analysis, and adaptive design. Dr. Xia has pre-
sented her work at a variety of professional conferences and published them
in many peer-reviewed journals and books. She is a member of the PhRMA
SPERT (Safety Planning, Evaluation, and Reporting Team), the Council for
International Organizations of Medical Sciences (CIOMS) X Working Group,
the Drug Information Association (DIA) Bayesian Scientific Working Group

xi
xii Editors

where she co-leads the safety subteam, and the Biostatistics Workgroup for
CTTI (Clinical Trials Transformation Initiative)’s IND (Investigational New
Drug) Safety Project. Dr. Xia has taught a short course entitled “Bayesian
Methods for Drug Safety Evaluation and Signal Detection” at the DIA/FDA
(Food and Drug Administration) Statistics Forum 2014. She holds an MS
and a PhD in biostatistics from the University of Minnesota, and a medical
degree from Peking University, China.
Contributors

Mary Banach Christy Chuang-Stein

Department of Biostatistics Statistical Research and Consulting
Vanderbilt University School of Center
Medicine Pfizer
Nashville, Tennessee Kalamazoo, Michigan

Jesse A. Berlin Jason T. Connor

Department of Epidemiology Berry Consultants
Johnson & Johnson Austin, Texas
Titusville, New Jersey and

Jordan C. Brooks College of Medicine

Life Expectancy Project University of Central Florida
San Francisco, California Orlando, Florida

Brenda Crowe
Bradley P. Carlin
Eli Lilly and Company
Division of Biostatistics
Indianapolis, Indiana
University of Minnesota
Minneapolis, Minnesota
Susan P. Duke
Benefit Risk Evaluation
Aloka G. Chakravarty
Global Clinical Safety and
Division of Biometrics VII
Pharmacovigilance
Office of Biostatistics
GlaxoSmithKline
Office of Translational Sciences
Research Triangle Park, North
Center for Drug Evaluation and
Carolina
Research
U.S. Food and Drug Administration
Alan S. Go
Silver Spring, Maryland
Division of Research
Kaiser Permanente
Ming-Hui Chen Oakland, California
Department of Statistics
University of Connecticut Hisham Hamadeh
Storrs, Connecticut Amgen, Inc.
Thousand Oaks, California
Max Cherny
Clinical Programming Violeta Hennessey
GlaxoSmithKline Amgen, Inc.
King of Prussia, Pennsylvania Thousand Oaks, California

xiii
xiv Contributors

Hwanhee Hong Kazuhiko Kuribayashi

Department of Mental Health Pfizer
Johns Hopkins Bloomberg School Tokyo, Japan
of Public Health
Baltimore, Maryland Mark Levenson
Division of Biometrics VII
Liping Huang Office of Biostatistics
CSL Behring Office of Translational Sciences
King of Prussia, Pennsylvania Center for Drug Evaluation and
Research
U.S. Food and Drug Administration
Joseph G. Ibrahim
Silver Spring, Maryland
Department of Biostatistics
University of North Carolina
Thomas Liu
at Chapel Hill
Amgen, Inc.
Chapel Hill, North Carolina
Thousand Oaks, California

Yoichi Ii David Madigan

Pfizer Department of Statistics
Tokyo, Japan Columbia University
New York, New York
Qi Jiang
and
Amgen, Inc.
Thousand Oaks, California Observational Medical Outcomes
Partnership
Norisuke Kawai Foundation for the National
Pfizer Institutes of Health
Tokyo, Japan Bethesda, Maryland

Chunlei Ke Mary Nilsson

Amgen, Inc. Eli Lilly and Company
Thousand Oaks, California Indianapolis, Indiana

Karen L. Price
Osamu Komiyama Eli Lilly and Company
Pfizer Indianapolis, Indiana
Tokyo, Japan
Hong Qiu
Jürgen Kübler Department of Epidemiology
CSL Behring Janssen Research and Development
Marburg, Germany Titusville, New Jersey
Contributors xv

Patrick Ryan Steven Snapinn

Janssen Research and Development Amgen, Inc.
Titusville, New Jersey Thousand Oaks, California
and
Paul E. Stang
Observational Medical Outcomes Department of Epidemiology
Partnership Janssen Research and Development
Foundation for the National Titusville, New Jersey
Institutes of Health
Bethesda, Maryland
John Sullivan
Mark Schactman Global Regulatory Affairs and Safety
Statistics Collaborative, Inc. Washington, DC
Washington, DC
Mark J. van der Laan
Martijn Schuemie Division of Biostatistics
Janssen Research and Development University of California, Berkeley
Titusville, New Jersey Berkeley, California
and
José M. Vega
Observational Medical Outcomes
Merck Research Laboratories
Partnership
North Wales, Pennsylvania
Foundation for the National
Institutes of Health
Bethesda, Maryland Wei Wang
Eli Lilly Canada, Inc.
Seta Shahin Toronto, Ontario, Canada
Amgen, Inc.
Thousand Oaks, California Janet Wittes
Statistics Collaborative, Inc.
Atsuko Shibata Washington, DC
Amgen, Inc.
Thousand Oaks, California
H. Amy Xia
Daniel E. Singer Amgen, Inc.
Department of Medicine Thousand Oaks, California
Massachusetts General Hospital
Boston, Massachusetts
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