Microarrays in Diagnostics and Biomarker Development

Microarrays in Diagnostics and Biomarker Development

.

Editor Microarrays in Diagnostics and Biomarker Development Current and Future Applications

Editor CoReBio PACA Luminy Science Park 13288 Marseille Cedex 9 France ISBN 978-3-642-28202-7 ISBN 978-3-642-28203-4 (ebook) DOI 10.1007/978-3-642-28203-4 Springer Heidelberg New York Dordrecht London Library of Congress Control Number: 2012936972 # Springer-Verlag Berlin Heidelberg 2012 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com)

Preface This is the second time I assemble a book on microarrays for Springer almost exactly 10 years after the first one (DNA microarrays: Gene expression applications. Springer Berlin Heidelberg 2001). During this interval, we have seen tremendous changes in the landscape of genomics and molecular biology. The first human genome sequence, with its revelations on gene number and relatively low human genetic diversity, was shortly followed by extensive investigation of single nucleotide polymorphisms in our DNA and, with the help of more and more complex SNP arrays, by extensive whole-genome association studies (GWAS). These have uncovered many gene/phenotype correlations, but have also revealed how limited our understanding of the functional genome still is. The importance of non-coding transcripts and of epigenetic modifications of our DNA has been realised. And very recently, DNA sequencing technology has made tremendous progress, to the point that the 1,000-dollar genome is in sight and that clinical use of whole-genome or exome sequencing is becoming significant (and is in fact competing with some uses of arrays). Meanwhile, clinical applications of DNA microarrays have developed, but not exactly in the directions anticipated 10 years ago and not quite at the level predicted by some analysts. Other microarrays using proteins, antibodies, peptide, or aptamer molecules as probes have made significant advances in spite of technical problems, and now have an impact not only in research but also in the clinic and in biomarker development. This new book includes 13 main chapters, and covers essentially all types of arrays. It is focussed on entities that are in actual clinical use, or quite close to it thus it does not discuss, for example, complex SNP arrays that remain essentially a research tool. It does present some very recent developments, such as peptide or aptamer arrays, or also miniaturisation towards nanoarrays, that I see as having great potential in medicine even though their current presence is still limited. It discusses in detail very important issues in bioinformatics and in statistical analysis of array data, as well as the hurdles faced in the commercialisation of array-based tests and the vexing IP issues associated with these activities. v

vi Preface I believe this book will be useful to current array users who wish to have a complete view of the field, to newcomers who attempt to make the best choice between different technologies, and to academic scientists who engage in technology transfer activities and need to evaluate the hurdles involved in this process. I am especially grateful to the authors, my colleagues, who kindly accepted to undertake the absorbing task of writing a chapter, especially at a time where tight funding means that they are extremely busy preparing grant applications. And, of course, the organisational support from Springer to overcome the 1,001 small problems encountered in the production of this book is gratefully acknowledged. Marseille, France

Contents 1 The Microarray Paradigm and Its Various Implementations... 1 Part I DNA Arrays 2 DNA Arrays in Many Guises... 11 3 Expression Profiling for Diagnostics... 21 4 Genotype Characterisation for Diagnostics... 29 5 Array-CGH and SNP-Arrays, the New Karyotype... 39 Karoly Szuhai Part II Protein (Antigen and Antibody) and Peptide Arrays 6 Protein Microarrays and Their Potential Clinical Applications in the Era of Personalized Medicine... 55 Hong Zhang and Steven Pelech 7 Peptide Arrays... 81 Hong Zhang, Steven Pelech, Rob Ruijtenbeek, Thomas Felgenhauer, Ralf Bischoff, Frank Breitling, and Volker Stadler 8 Slow Off-Rate Modified Aptamer Arrays for Biomarker Discovery and Diagnostic Applications... 113 Jeffrey J. Walker, Edward N. Brody, and Larry Gold vii

viii Contents Part III Other Types of Arrays 9 Tissue Microarrays for Translational Research... 135 Ronald Simon and Martina Mirlacher 10 Recent and Future Developments of Microarrays: Miniaturization and Lab-on-Chip Approaches... 153 Inbal Tsarfati-BarAd and Levi A. Gheber Part IV Data Analysis, Commercial and Regulatory Aspects 11 Analysis of Array Data and Clinical Validation of Array-Based Assays... 171 Benjamin Haibe-Kains and John Quackenbush 12 Challenges in the Commercialization of Array-Based Tests... 211 Justin Petrone 13 Genes, Microarrays, and Patents... 229 Justin Petrone Concluding Remarks... 237 Index... 239