Table Of Content

Design and Analysis of Clinical Trials for Predictive Medicine 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 Development Applied Meta-Analysis with R Andreas Sashegyi, James Felli, and Ding-Geng (Din) Chen and Karl E. Peace Rebecca Noel Basic Statistics and Pharmaceutical Biosimilars: Design and Analysis of Statistical Applications, Second Edition Follow-on Biologics James E. De Muth Shein-Chung Chow Bayesian Adaptive Methods for Biostatistics: A Computing Approach Clinical Trials Stewart J. Anderson Scott M. Berry, Bradley P. Carlin, J. Jack Lee, and Peter Muller Causal Analysis in Biomedicine and Epidemiology: Based on Minimal Bayesian Analysis Made Simple: An Excel Sufficient Causation GUI for WinBUGS Mikel Aickin Phil Woodward Clinical and Statistical Considerations Bayesian Methods for Measures of in Personalized Medicine Agreement Claudio Carini, Sandeep Menon, Lyle D. Broemeling and Mark Chang Bayesian Methods in Epidemiology Lyle D. Broemeling Clinical Trial Data Analysis using R DNA Microarrays and Related Genomics Ding-Geng (Din) Chen and Karl E. Peace Techniques: Design, Analysis, and Interpretation of Experiments Clinical Trial Methodology David B. Allison, Grier P. Page, Karl E. Peace and Ding-Geng (Din) Chen T. Mark Beasley, and Jode W. Edwards Computational Methods in Biomedical Dose Finding by the Continual Research Reassessment Method Ravindra Khattree and Dayanand N. Naik Ying Kuen Cheung Computational Pharmacokinetics Elementary Bayesian Biostatistics Anders Källén Lemuel A. Moyé Confidence Intervals for Proportions and Frailty Models in Survival Analysis Related Measures of Effect Size Andreas Wienke Robert G. Newcombe Generalized Linear Models: A Bayesian Controversial Statistical Issues in Perspective Clinical Trials Dipak K. Dey, Sujit K. Ghosh, Shein-Chung Chow and Bani K. Mallick Data and Safety Monitoring Committees Handbook of Regression and Modeling: in Clinical Trials Applications for the Clinical and Jay Herson Pharmaceutical Industries Design and Analysis of Animal Studies in Daryl S. Paulson Pharmaceutical Development Inference Principles for Biostatisticians Shein-Chung Chow and Jen-pei Liu Ian C. Marschner Design and Analysis of Bioavailability and Interval-Censored Time-to-Event Data: Bioequivalence Studies, Third Edition Methods and Applications Shein-Chung Chow and Jen-pei Liu Ding-Geng (Din) Chen, Jianguo Sun, Design and Analysis of Bridging Studies and Karl E. Peace Jen-pei Liu, Shein-Chung Chow, Joint Models for Longitudinal and Time- and Chin-Fu Hsiao to-Event Data: With Applications in R Design and Analysis of Clinical Trials for Dimitris Rizopoulos Predictive Medicine Measures of Interobserver Agreement Shigeyuki Matsui, Marc Buyse, and Reliability, Second Edition and Richard Simon Mohamed M. Shoukri Design and Analysis of Clinical Trials with Medical Biostatistics, Third Edition Time-to-Event Endpoints A. Indrayan Karl E. Peace Meta-Analysis in Medicine and Health Design and Analysis of Non-Inferiority Policy Trials Dalene Stangl and Donald A. Berry Mark D. Rothmann, Brian L. Wiens, and Ivan S. F. Chan Mixed Effects Models for the Population Approach: Models, Tasks, Methods and Difference Equations with Public Health Tools Applications Marc Lavielle Lemuel A. Moyé and Asha Seth Kapadia Monte Carlo Simulation for the DNA Methylation Microarrays: Pharmaceutical Industry: Concepts, Experimental Design and Statistical Algorithms, and Case Studies Analysis Mark Chang Sun-Chong Wang and Arturas Petronis Multiple Testing Problems in Statistical Analysis of Human Growth Pharmaceutical Statistics and Development Alex Dmitrienko, Ajit C. Tamhane, Yin Bun Cheung and Frank Bretz Statistical Design and Analysis of Noninferiority Testing in Clinical Trials: Stability Studies Issues and Challenges Shein-Chung Chow Tie-Hua Ng Statistical Evaluation of Diagnostic Optimal Design for Nonlinear Response Performance: Topics in ROC Analysis Models Kelly H. Zou, Aiyi Liu, Andriy Bandos, Valerii V. Fedorov and Sergei L. Leonov Lucila Ohno-Machado, and Howard Rockette Patient-Reported Outcomes: Statistical Methods for Clinical Trials Measurement, Implementation and Mark X. Norleans Interpretation Statistical Methods in Drug Combination Joseph C. Cappelleri, Kelly H. Zou, Studies Andrew G. Bushmakin, Jose Ma. J. Alvir, Wei Zhao and Harry Yang Demissie Alemayehu, and Tara Symonds Statistics in Drug Research: Quantitative Evaluation of Safety in Drug Methodologies and Recent Development: Design, Analysis and Developments Reporting Shein-Chung Chow and Jun Shao Qi Jiang and H. Amy Xia Statistics in the Pharmaceutical Industry, Randomized Clinical Trials of Third Edition Nonpharmacological Treatments Ralph Buncher and Jia-Yeong Tsay Isabelle Boutron, Philippe Ravaud, and Survival Analysis in Medicine and David Moher Genetics Randomized Phase II Cancer Clinical Jialiang Li and Shuangge Ma Trials Theory of Drug Development Sin-Ho Jung Eric B. Holmgren Sample Size Calculations for Clustered Translational Medicine: Strategies and and Longitudinal Outcomes in Clinical Statistical Methods Research Dennis Cosmatos and Shein-Chung Chow Chul Ahn, Moonseong Heo, and Song Zhang Sample Size Calculations in Clinical Research, Second Edition Shein-Chung Chow, Jun Shao and Hansheng Wang Design and Analysis of Clinical Trials for Predictive Medicine Edited by Shigeyuki Matsui Marc Buyse Richard Simon 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: 20150204 International Standard Book Number-13: 978-1-4665-5816-8 (eBook - PDF) This book contains information obtained from authentic and highly regarded sources. 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Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com Contents Preface.......................................................................................................................xi Editors....................................................................................................................xiii Contributors............................................................................................................xv Section I Introductory Overview 1. Clinical Trials for Predictive Medicine: New Paradigms and Challenges.................................................................................................3 Richard Simon, Shigeyuki Matsui, and Marc Buyse 2. An Industry Statistician’s Perspective on Personalized Health Care Drug Development.................................................................11 Jane Fridlyand, Ru-Fang Yeh, Howard Mackey, Thomas Bengtsson, Paul Delmar, Greg Spaniolo, and Grazyna Lieberman 3. Analytical Validation of In Vitro Diagnostic Tests................................33 Robert Becker, Jr. Section II Early Clinical Trials Using Biomarkers 4. Phase I Dose-Finding Designs and Their Applicability to Targeted Therapies........................................................................................53 Takashi Daimon, Akihiro Hirakawa, and Shigeyuki Matsui 5. An Overview of Phase II Clinical Trial Designs with Biomarkers.......71 Lisa McShane and Sally Hunsberger 6. Bayesian Adaptive Methods for Clinical Trials of Targeted Agents.......89 Peter Thall 7. Outcome-Adaptive Randomization in Early Clinical Trials..............111 Edward Korn and Boris Freidlin 8. Challenges of Using Predictive Biomarkers in Clinical Trials..........129 Sumithra Mandrekar and Daniel Sargent vii viii Contents Section III Phase III Randomized Clinical Trials Using Biomarkers 9. Comparison of Randomized Clinical Trial Designs for Targeted Agents...........................................................................................147 Antje Hoering, Mike LeBlanc, and John Crowley 10. Phase III All-Comers Clinical Trials with a Predictive Biomarker.......165 Shigeyuki Matsui, Yuki Choai, and Takahiro Nonaka 11. Evaluation of Clinical Utility and Validation of Gene Signatures in Clinical Trials.....................................................................187 Stefan Michiels and Federico Rotolo Section IV Analysis of High-Dimensional Data and Genomic Signature Developments 12. Statistical Issues in Clinical Development and Validation of Genomic Signatures....................................................................................207 Shigeyuki Matsui 13. Univariate Analysis for Gene Screening: Beyond Multiple Testing......................................................................................227 Hisashi Noma and Shigeyuki Matsui 14. Statistical and Machine-Learning Methods for Class Prediction in High Dimension.....................................................................................253 Osamu Komori and Shinto Eguchi 15. Survival Risk Prediction Using High-Dimensional Molecular Data.............................................................................................271 Harald Binder, Thomas Gerds, and Martin Schumacher Section V Randomized Trials with Biomarker Development and Validation 16. Adaptive Clinical Trial Designs with Biomarker Development and Validation..............................................................................................295 Boris Freidlin and Richard Simon 17. Development and Validation of Continuous Genomic Signatures in Randomized Clinical Trials............................................315 Shigeyuki Matsui Contents ix Section VI Evaluation of Surrogate Biomarkers 18. Biomarker-Based Surrogate Endpoints...................................................333 Marc Buyse, Tomasz Burzykowski, Geert Molenberghs, and Ariel Alonso Index......................................................................................................................371