Computational Methods in Biomedical Research 1st Edition

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 iii

Published Titles

1. Design and Analysis of Animal Studies in Pharmaceutical Development,

Shein-Chung Chow and Jen-pei Liu
2. Basic Statistics and Pharmaceutical Statistical Applications,
James E. De Muth
3. Design and Analysis of Bioavailability and Bioequivalence Studies,
Second Edition, Revised and Expanded, Shein-Chung Chow and Jen-pei Liu
4. Meta-Analysis in Medicine and Health Policy, Dalene K. Stangl and
Donald A. Berry
5. Generalized Linear Models: A Bayesian Perspective, Dipak K. Dey,
Sujit K. Ghosh, and Bani K. Mallick
6. Difference Equations with Public Health Applications, Lemuel A. Moyé
and Asha Seth Kapadia
7. Medical Biostatistics, Abhaya Indrayan and Sanjeev B. Sarmukaddam
8. Statistical Methods for Clinical Trials, Mark X. Norleans
9. Causal Analysis in Biomedicine and Epidemiology: Based on Minimal
Sufficient Causation, Mikel Aickin
10. Statistics in Drug Research: Methodologies and Recent Developments,
Shein-Chung Chow and Jun Shao
11. Sample Size Calculations in Clinical Research, Shein-Chung Chow, Jun Shao, and
Hansheng Wang
12. Applied Statistical Design for the Researcher, Daryl S. Paulson
13. Advances in Clinical Trial Biostatistics, Nancy L. Geller
14. Statistics in the Pharmaceutical Industry, Third Edition, Ralph Buncher
and Jia-Yeong Tsay
15. DNA Microarrays and Related Genomics Techniques: Design, Analysis, and Interpretation
of Experiments, David B. Allsion, Grier P. Page, T. Mark Beasley, and Jode W. Edwards
16. Basic Statistics and Pharmaceutical Statistical Applications, Second Edition, James E.
De Muth
17. Adaptive Design Methods in Clinical Trials, Shein-Chung Chow and
Mark Chang
18. Handbook of Regression and Modeling: Applications for the Clinical and Pharmaceutical
Industries, Daryl S. Paulson
19. Statistical Design and Analysis of Stability Studies, Shein-Chung Chow
20. Sample Size Calculations in Clinical Research, Second Edition, Shein-Chung Chow,
Jun Shao, and Hansheng Wang
21. Elementary Bayesian Biostatistics, Lemuel A. Moyé
22. Adaptive Design Theory and Implementation Using SAS and R, Mark Chang
23. Computational Pharmacokinetics, Anders Kallen

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 v

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Contents

Series Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

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

1 Microarray Data Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Susmita Datta, Somnath Datta, Rudolph S. Parrish, and
Caryn M. Thompson

2 Machine Learning Techniques for Bioinformatics:

Fundamentals and Applications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Jarosław Meller and Michael Wagner

3 Machine Learning Methods for Cancer Diagnosis and

Prognostication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Anne-Michelle Noone and Mousumi Banerjee

4 Protein Profiling for Disease Proteomics with Mass

Spectrometry: Computational Challenges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Dayanand N. Naik and Michael Wagner

5 Predicting US Cancer Mortality Counts Using State

Space Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Kaushik Ghosh, Ram C. Tiwari, Eric J. Feuer, Kathleen A. Cronin,
and Ahmedin Jemal

6 Analyzing Multiple Failure Time Data Using SAS® Software . . . . . 153

Joseph C. Gardiner, Lin Liu, and Zhehui Luo

7 Mixed-Effects Models for Longitudinal Virologic and

Immunologic HIV Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
Florin Vaida, Pulak Ghosh, and Lin Liu

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viii Contents

8 Bayesian Computational Methods in Biomedical Research. . . . . . . . . 211

Hedibert F. Lopes, Peter Müller, and Nalini Ravishanker

9 Sequential Monitoring of Randomization Tests . . . . . . . . . . . . . . . . . . . . . . 261

Yanqiong Zhang and William F. Rosenberger

10 Proportional Hazards Mixed-Effects Models and Applications . . . . 297

Ronghui Xu and Michael Donohue

11 Classification Rules for Repeated Measures Data from

Biomedical Research. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323
Anuradha Roy and Ravindra Khattree

12 Estimation Methods for Analyzing Longitudinal Data

Occurring in Biomedical Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371
N. Rao Chaganty and Deepak Mav

Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 401

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Series Introduction

The primary objectives of the Biostatistics Book Series are to provide useful
reference books for researchers and scientists in academia, industry, and gov-
ernment, and also to offer textbooks for undergraduate and graduate courses
in the area of biostatistics. This book series will provide comprehensive and
unified presentations of statistical designs and analyses of important applic-
ations in biostatistics, such as those in biopharmaceuticals. A well-balanced
summary will be given of current and recently developed statistical meth-
ods and interpretations for both statisticians and researchers or scientists
with minimal statistical knowledge who are engaged in the field of applied
biostatistics. The series is committed to providing easy-to-understand, state-
of-the-art references and textbooks. In each volume, statistical concepts and
methodologies will be illustrated through real-world examples.
In the last decade, it was recognized that increased spending on biomed-
ical research does not reflect an increase in the success rate of pharmaceutical
development. On March 16, 2004, the FDA released a report addressing
the recent slowdown in innovative medical therapies submitted to the FDA
for approval, “Innovation/Stagnation: Challenge and Opportunity on the
Critical Path to New Medical Products.” The report describes the urgent need
to modernize the medical product development process—the critical path—to
make product development more predictable and less costly. Two years later,
the FDA released a Critical Path Opportunities List that outlines 76 initial pro-
jects (under six broad topic areas) to bridge the gap between the quick pace of
new biomedical discoveries and the slower pace at which those discoveries
are currently developed into therapies. Among the six broad topic areas, bet-
ter evaluation tool (development of biomarker), streamlining clinical trial (the
use of adaptive design methods), and harnessing bioinformatics (the use of
computational biology) are considered the top three challenges for increasing
the probability of success in pharmaceutical research and development.
This volume provides useful approaches for implementation of target
clinical trials in pharmaceutical research and development. It covers stat-
istical methods for various computational topics such as biomarker devel-
opment, sequential monitoring, proportional hazard mixed-effects models,
and Bayesian approach in pharmaceutical research and development. It
would be beneficial to biostatisticians, medical researchers, pharmaceutical

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x Series Introduction

scientists, and reviewers in regulatory agencies who are engaged in the areas
of pharmaceutical research and development.

Shein-Chung Chow

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Preface

This edited volume is a collection of chapters covering some of the important

computational topics with special reference to biomedical applications. Rapid
advances in ever-changing biomedical research and methodological statistical
developments that must support these advances make it imperative that from
time to time a cohesive account of new computational schemes is made avail-
able for users to implement these methodologies in the particular biomedical
context or problem. The present volume is an attempt to fill this need.
Realizing the vastness of the area itself, there is no pretension to be exhaust-
ive in terms of the general field or even in terms of a topic represented by a
chapter within this field; such a task, while also requiring hundreds of collab-
orators, would require a collection of several volumes of similar size. Hence
the selection made here represents our personal view of what the most import-
ant topics are, in terms of their applicability and potential in the near future.
With this in mind, the chapters are arranged accordingly, with the works of
immediate applicability appearing first. These are followed by more theor-
etical advances and computational schemes that are yet to be developed in
satisfactory forms for general applications.
Work of this magnitude could not have been accomplished without the
help of many people. We wish to thank our referees for painstakingly
going through the chapters as a gesture of academic goodwill. Theresa Del
Forn of Taylor & Francis Group, was most helpful and patient with our
repeatedly broken promises of meeting the next deadline. Our families have
provided their sincere support during this project and we appreciate their
understanding as well.

Ravindra Khattree, Rochester, Michigan

Dayanand N. Naik, Norfolk, Virginia

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Editors

Ravindra Khattree, professor of statistics at Oakland University, Rochester,

Michigan, received his initial graduate training at the Indian Statistical
Institute. He received his PhD from the University of Pittsburgh in 1985.
He is the author or coauthor of numerous research articles on theoretical
and applied statistics in various national and international journals. His
research interests include multivariate analysis, experimental designs, quality
control, repeated measures, and statistical inference. In addition to teaching
graduate and undergraduate courses, Dr. Khattree regularly consults with
industry, hospitals, and academic researchers on various applied statistics
problems. He is a chief editor of the Journal of Statistics and Applications, editor
of InterStat, an online statistics journal, and an associate editor of the Journal
of Statistical Theory and Practice. For many years, he also served as an associate
editor for the Communications in Statistics. He is a Fellow of the American
Statistical Association, an elected member of the International Statistical
Institute, and a winner of the Young Statistician Award from International
Indian Statistical Association. Dr. Khattree is a coauthor of two books, both
with Dr. D. N. Naik, titled Applied Multivariate Statistics with SAS Software
(Second Edition) and Multivariate Data Reduction and Discrimination with SAS
Software, both copublished by SAS Press/Wiley. He has also coedited, with
Dr. C. R. Rao, the Handbook of Statistics 22: Statistics in Industry, published by
North Holland.
Dayanand N. Naik is professor of statistics at Old Dominion University,
Norfolk, Virginia. He received his MS degree in statistics from Karnatak
University, Dharwad, India, and PhD in statistics from the University of
Pittsburgh in 1985. He has published extensively in several well-respected
journals and advised numerous students for their PhD in statistics. His
research interests include multivariate analysis, linear models, quality con-
trol, regression diagnostics, repeated measures, and growth curve models.
Dr. Naik is an editor of InterStat, a statistics journal on the Internet, and
an associate editor of Communications in Statistics. Dr. Naik is also actively
involved in statistical consulting and collaborative research. He is an elected
member of International Statistical Institute and is very active in American
Statistical Association activities. Dr. Naik is coauthor of two books, both with
Dr. Khattree, titled Applied Multivariate Statistics with SAS Software (Second
Edition) and Multivariate Data Reduction and Discrimination with SAS Software,
both copublished by SAS Press/Wiley.

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Contributors

Mousumi Banerjee Department of Biostatistics, School of Public Health,

University of Michigan, Ann Arbor, Michigan

N. Rao Chaganty Department of Mathematics and Statistics, Old Dominion

University, Norfolk, Virginia

Kathleen A. Cronin Statistical Research and Applications Branch, National

Cancer Institute, Bethesda, Maryland

Somnath Datta Department of Bioinformatics and Biostatistics, School

of Public Health and Information Sciences, University of Louisville,
Louisville, Kentucky

Susmita Datta Department of Bioinformatics and Biostatistics, School of

Public Health and Information Sciences, University of Louisville, Louis-
ville, Kentucky

Michael Donohue Division of Biostatistics and Bioinformatics, Department

of Family and Preventive Medicine, University of California at San Diego,
La Jolla, California

Eric J. Feuer Statistical Research and Applications Branch, National Cancer

Institute, Bethesda, Maryland

Joseph C. Gardiner Division of Biostatistics, Department of Epidemiology,

Michigan State University, East Lansing, Michigan

Kaushik Ghosh Department of Mathematical Sciences, University of

Nevada at Las Vegas, Las Vegas, Nevada

Pulak Ghosh Department of Mathematics and Statistics, Georgia State

University, Atlanta, Georgia

Ahmedin Jemal Department of Epidemiology and Surveillance Research,

American Cancer Society, Atlanta, Georgia

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xvi Contributors

Ravindra Khattree Department of Mathematics and Statistics, Oakland

University, Rochester, Michigan

Lin Liu Division of Biostatistics, Department of Epidemiology, Michigan

State University, East Lansing, Michigan

Lin Liu Department of Family and Preventive Medicine, University of

California at San Diego, La Jolla, California

Hedibert F. Lopes Graduate School of Business, University of Chicago,

Chicago, Illinois

Zhehui Luo Division of Biostatistics, Department of Epidemiology,

Michigan State University, East Lansing, Michigan

Deepak Mav Constella Group, Inc., Durham, North Carolina

Jarosław Meller Division of Biomedical Informatics, Cincinnati Children’s

Hospital Research Foundation, Cincinnati, Ohio; Department of Inform-
atics, Nicholas Copernicus University, Torun, Poland; and Department of
Environmental Health, University of Cincinnati, Ohio

Peter Müller Department of Biostatistics, The University of Texas,

M. D. Anderson Cancer Center, Houston, Texas

Dayanand N. Naik Department of Mathematics and Statistics, Old Domin-

ion University, Norfolk, Virginia

Anne-Michelle Noone Department of Biostatistics, School of Public

Health, University of Michigan, Ann Arbor, Michigan

Rudolph S. Parrish Department of Bioinformatics and Biostatistics, School

of Public Health and Information Sciences, University of Louisville,
Louisville, Kentucky

Nalini Ravishanker Department of Statistics, University of Connecticut,

Storrs, Connecticut

William F. Rosenberger Department of Statistics, The Volgenau School

of Information Technology and Engineering, George Mason University,
Fairfax, Virginia

Anuradha Roy Department of Management Science and Statistics, The

University of Texas at San Antonio, San Antonio, Texas

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