DNA Arrays: Technologies and Experimental Strategies

173 Pages·2001·5.65 MB·English

by  Grigorenko E.V.

DNA ARRAYS
TECHNOLOGIES AND EXPERIMENTAL
STRATEGIES
Elena V. Grigorenko
Edited by
CRC PR ESS
Boca Raton London New York Washington, D.C.
Library of Congress Cataloging-in-Publication Data
DNA arrays : technologies and experimental strategies / edited by Elena V. Grigorenko.
p. cm. -- (Methods & new frontiers in neuroscience series)
Includes bibliographical references and index.
ISBN 0-8493-2285-5 (alk. paper)
1. DNA microarrays. I. Grigorenko, Elena V. II. Series.
QP624.5.D726 D624 2001
572.8'65--dc21 2001043455
CIP
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Series Preface
Our goal in creating the Methods & New Frontiers in Neuroscience Series is to
present the insights of experts on emerging experimental techniques and theoretical
concepts that are, or will be, at the vanguard of neuroscience. Books in the series
will cover topics ranging from methods to investigate apoptosis, to modern tech-
niques for neural ensemble recordings in behaving animals. The series will also
cover new and exciting multidisciplinary areas of brain research, such as computa-
tional neuroscience and neuroengineering, and will describe breakthroughs in clas-
sical fields like behavioral neuroscience. We want these books to be what every
neuroscientist will use in order to get acquainted with new methodologies in brain
research. These books can be given to graduate students and postdoctoral fellows
when they are looking for guidance to start a new line of research.
The series will consist of case-bound books of approximately 250 pages. Each
book will be edited by an expert and will consist of chapters written by the leaders
in a particular field. The books will be richly illustrated and contain comprehensive
bibliographies. Each chapter will provide substantial background material relevant
to the particular subject. Hence, these are not going to be only “methods books.”
They will contain detailed “tricks of the trade” and information as to where these
methods can be safely applied. In addition, they will include information about
where to buy equipment, Web sites that will be helpful in solving both practical and
theoretical problems, and special boxes in each chapter that will highlight topics
that need to be emphasized along with relevant references.
We are working with these goals in mind and hope that as the volumes become
available, the effort put in by us, the publisher, the book editors, and individual
authors will contribute to the further development of brain research. The extent to
which we achieve this goal will be determined by the utility of these books.
Sidney A. Simon, Ph.D.
Miguel A. L. Nicolelis, M.D., Ph.D.
Duke University
Series Editors
©2002 CRC Press LLC
Preface
With advances in high-density DNA microarray technology, it has become possible
to screen large numbers of genes to see whether or not they are active under various
conditions. This is a gene-expression profiling approach that, over the past few years,
has revolutionized the molecular biology field. The thinking is that any alterations
in a physiological state are dictated by the expression of thousands of genes, and
that microarray analysis allows that behavior to be revealed and to predict the clinical
consequences. This rationale is sound enough, but until now it has not been sub-
stantiated by many experiments. The expectations for microarray technology are
also high for prediction of better definition of patient groups, based on expression
profiling. It is of obvious importance for assessing the efficacy of various treatments
and to create “personalized” medicine.
The field of microarray technology presents a tremendous technical challenge
for both academic institutions and industry. This book includes reviews of traditional
nylon-based microarray assays as well as new, emerging technologies such as
electrochemical detection of nucleic acid hybridization. Novel platforms such as
oligonucleotide arrays are being developed, and companies that have never engaged
in the life science industry are entering this rapidly growing market (see Dorris
et al.’s review on oligonucleotide microarrays). Indeed, time will show which of
the emerging technologies will have a significant impact on the future of microarray
research.
Because microarray analysis is a high-throughput technology, the amount of
data being generated is expanding at a tremendous rate. The handling and analysis
of data require elaborate databases, query tools, and data visualization software.
This book contains several examples of how a large set of data can be mined using
different statistical tools (for details, see Chapters 6 and 7). Readers are also provided
with a reproducible protocol for amplification of limited amounts of RNA in micro-
array-based analysis. The primary limitation of microrray technology — usage of
a large amount of RNA — could be overcome with the technique described in
Chapter 5 by Potier and colleagues, who in 1992 pioneered the RT-PCR technique
for profiling gene expression in single neurons.
In summary, readers from different scientific fields and working environments
will find this book a useful addition to the few books currently available. I am
indebted to CRC Press Senior Editor Barbara Norwitz, who has given me unwavering
support and brought common sense, order, and timeliness to a process that sometimes
threatened to fall out of control. I also owe special thanks to Miguel Nicolelis for
many good suggestions and Alexandre Kirillov for the encouragement and sustaining
enthusiasm during the work on this book.
©2002 CRC Press LLC
Editor
Elena V. Grigorenko, Ph.D., is a Scientist in the Technology Development Group
at Millennium Pharmaceuticals, Inc., Cambridge, Massachusetts. She did her under-
graduate studies in Russia at the Saratov State University and at the Moscow State
University. Dr. Grigorenko’s graduate research in bioenergetics was conducted in
Dr. Maria N. Kondrashova’s laboratory at the Institute of Biological Physics at
Pushchino — a well-known biological center of the Russian Academy of Sciences.
Dr. Grigorenko was a recipient of Sigma-Tau (Italy) and Chilton Foundation (Dallas,
Texas) fellowships and she was a faculty member at the Wake Forest University
School of Medicine, Winston-Salem, North Carolina. Currently her research inter-
ests are focused on applications of biochip and nanotechnologies for a drug discov-
ery process.
©2002 CRC Press LLC
Contributors
Bruno Cauli, Ph.D. Willard M. Freeman, Ph.D.
Neurobiologie et Diversité Department of Physiology and
Cellulaire Pharmacology
ESPCI Wake Forest University School of
Paris Medicine
Winston-Salem, North Carolina
Chris Clayton, Ph.D.
Glaxo Wellcome Stefanie Fuhrman, Ph.D.
Stevenage, U.K. Incyte Genomics, Inc.
Palo Alto, California
Sam A. Deadwyler, Ph.D.
Department of Physiology and Alexander Gee, Ph.D.
Pharmacology AnVil Informatics, Inc.
Wake Forest University School of Lowell, Massachusetts
Medicine
Winston-Salem, North Carolina Natalie Gibelin, Ph.D.
Neurobiologie et Diversité
Frédéric Devaux, Ph.D. Cellulaire
Laboratorie de Génétique Moléculaire ESPCI
ENS Paris
Paris
Geoffroy Golfier, Ph.D.
David Dorris, Ph.D. Neurobiologie et Diversité
Motorola Life Sciences Cellulaire
Northbrook, Illinois ESPCI
Paris
Allen Eckhardt, Ph.D.
Xanthon, Inc. Elena V. Grigorenko, Ph.D.
Research Triangle Park, North Carolina Millennium Pharmaceuticals, Inc.
Cambridge, Massachusetts
Holger Eickhoff, Ph.D.
Max-Planck-Institut für Molekulare Georges Grinstein, Ph.D.
Genetik AnVil Informatics, Inc.
Berlin Lowell, Massachusetts
Eric Espenhahn, Ph.D. Bruce Hoff, Ph.D.
Xanthon, Inc. BioDiscovery, Inc.
Research Triangle Park, North Carolina Los Angeles, California
©2002 CRC Press LLC
Patrick Hoffman, Ph.D. Philippe Marc
AnVil Informatics, Inc. Laboratorie de Génétique Moléculaire
Lowell, Massachusetts ENS
Paris
C. Bret Jessee, Ph.D.
AnVil Informatics, Inc. Abhijit Mazumder, Ph.D.
Lowell, Massachusetts Motorola Life Sciences
Northbrook, Illinois
Josef Kittler, Ph.D.
University College of London Mary Napier, Ph.D.
London Xanthon, Inc.
Research Triangle Park, North Carolina
Sonia Kuhlmann, Ph.D.
Neurobiologie et Diversité Cellulaire Wilfried Nietfeld, Ph.D.
ESPCI Max-Planck-Institut für Molekulare
Paris Genetik
Berlin
Alexander Kuklin, Ph.D.
BioDiscovery, Inc. Eckhard Nordhoff, Ph.D.
Los Angeles, California Max-Planck-Institut für Molekulare
Genetik
Bertrand Lambolez Berlin
Neurobiologie et Diversité Cellulaire
ESPCI Lajos Nyarsik, Ph.D.
Paris Max-Planck-Institut für Molekulare
Genetik
Beatrice Le Bourdelles Berlin
Neuroscience Research Centre
Merck Sharp & Dohme Research Phil O’Neil, Ph.D.
Laboratories AnVil Informatics, Inc.
Harlow, United Kingdom Lowell, Massachusetts
Hans Lehrach, Ph.D. Natasha Popovich, Ph.D.
Max-Planck-Institut für Molekulare Xanthon, Inc.
Genetik Research Triangle Park, North Carolina
Berlin
Marie-Claude Potier, Ph.D.
Shoudan Liang Neurobiologie et Diversité Cellulaire
Incyte Genomics, Inc. ESPCI
Palo Alto, California Paris
Scott Magnuson, Ph.D. Ramesh Ramakrishnan, Ph.D.
Motorola Life Sciences Motorola Life Sciences
Northbrook, Illinois Northbrook, Illinois
©2002 CRC Press LLC
Jean Rossier, Ph.D. Kent E. Vrana, Ph.D.
Neurobiologie et Diversité Cellulaire Department of Physiology and
ESPCI Pharmacology
Paris Wake Forest University School of
Medicine
Ulrich Schneider, Ph.D. Winston-Salem, North Carolina
Max-Planck-Institut für Molekulare
Genetik Don Wallace, Ph.D.
Berlin Glaxo Wellcome
Stevenage, U.K.
Tim Sendera
Motorola Life Sciences Xiling Wen, Ph.D.
Northbrook, Illinois Incyte Genomics, Inc.
Palo Alto, California
Shishir Shah, Ph.D.
BioDiscovery, Inc. Robert Witwer, Ph.D.
Los Angeles, California Xanthon, Inc.
Research Triangle Park, North Carolina
Soheil Shams, Ph.D.
BioDiscovery, Inc.
Günther Zehetner, Ph.D.
Los Angeles, California
German Resource Centre and Primary
Database in the German Genome
Roland Somogyi, Ph.D.
Project
Molecular Mining Corporation
Berlin
Kingston, Ontario, Canada
Shou-Yuan Zhuang, Ph.D.
Holden Thorp, Ph.D.
Department of Physiology and
Department of Chemistry
Pharmacology
Kenan Laboratories
Wake Forest University School of
University of North Carolina at Chapel
Medicine
Hill
Winston-Salem, North Carolina
Chapel Hill, North Carolina
©2002 CRC Press LLC
Contents
Chapter 1
Technology Development for DNA Chips
Holger Eickhoff, Ulrich Schneider, Eckhard Nordhoff, Lajos Nyarsik,
Günther Zehetner, Wilfried Nietfeld, and Hans Lehrach
Chapter 2
Experimental Design for Hybridization Array Analysis of Gene Expression
Willard M. Freeman and Kent E. Vrana
Chapter 3
Oligonucleotide Array Technologies for Gene Expression Profiling
David Dorris, Ramesh Ramakrishnan, Tim Sendera, Scott Magnuson,
and Abhijit Mazumder
Chapter 4
Electrochemical Detection of Nucleic Acids
Allen Eckhardt, Eric Espenhahn, Mary Napier, Natasha Popovich,
Holden Thorp, and Robert Witwer
Chapter 5
DNA Microarrays in Neurobiology
Marie-Claude Potier, Geoffroy Golfier, Bruno Cauli, Natalie Gibelin,
Beatrice Le Bourdelles, Bertrand Lambolez, Sonia Kuhlmann, Philippe Marc,
Frédéric Devaux, and Jean Rossier
Chapter 6
High-Dimensional Visualization Support for Data Mining Gene
Expression Data
Georges Grinstein, C. Bret Jessee, Patrick Hoffman, Phil O’Neil,
and Alexander Gee
Chapter 7
Data Management in Microarray Fabrication, Image Processing,
and Data Mining
Alexander Kuklin, Shishir Shah, Bruce Hoff, and Soheil Shams
©2002 CRC Press LLC
Chapter 8
Zeroing in on Essential Gene Expression Data
Stefanie Fuhrman, Shoudan Liang, Xiling Wen, and Roland Somogyi
Chapter 9
Application of Arrayed Libraries for Analysis of Differential
Gene Expression Following Chronic Cannabinoid Exposure
Josef Kittler, Shou-Yuan Zhuang, Chris Clayton, Don Wallace,
Sam A. Deadwyler, and Elena V. Grigorenko
©2002 CRC Press LLC