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Modern Molecular Biology
Modern Molecular Biology
Applied Bioinformatics and Biostatistics in Cancer Research
Series editor: Jeanne Kowalski, Steven Piantadosi
For other titles published in this series, go to
www.springer.com/series/7616
Srinivasan Yegnasubramanian ● William B. IsaacsEditors
Modern Molecular Biology
Approaches for Unbiased Discovery in Cancer Research
EditorsSrinivasan YegnasubramanianDepartment of OncologySidney Kimmel Comprehensive Cancer CenterJohns Hopkins University, School of MedicineBaltimore, [email protected]
William B. IsaacsDepartment of Urology, Pharmacology, OncologySidney Kimmel Comprehensive Cancer CenterBrady Urological InstituteJohns Hopkins University, School of MedicineBaltimore, [email protected]
ISBN 978-0-387-69744-4 e-ISBN 978-0-387-69745-1DOI 10.1007/978-0-387-69745-1Springer New York Dordrecht Heidelberg London
Library of Congress Control Number: 2010933871
© Springer Science+Business Media, LLC 2010All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connec-tion with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden.The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights.
Printed on acid-free paper
Springer is part of Springer Science+Business Media (www.springer.com)
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Molecular biology has rapidly advanced since the discovery of the basic flow of information in life, from DNA to RNA to proteins. While there are several impor-tant and interesting exceptions to this general flow of information, the importance of these biological macromolecules in dictating the phenotypic nature of living creatures in health and disease is paramount. In the last one and a half decades, and particularly after the completion of the Human Genome Project, there has been an explosion of technologies that allow the broad characterization of these macromol-ecules in physiology, and the perturbations to these macromolecules that occur in diseases such as cancer. In this volume, we will explore the modern approaches used to characterize these macromolecules in an unbiased, systematic way. Such technologies are rapidly advancing our knowledge of the coordinated and compli-cated changes that occur during carcinogenesis, and are providing vital information that, when correctly interpreted by biostatistical/bioinformatics analyses, can be exploited for the prevention, diagnosis, and treatment of human cancers. The pri-mary purpose of this volume is to help bridge the gap between molecular biologists/cancer researchers and bioinformatics/computational biology researchers by pro-viding an overview of these technologies to those that are not yet familiar with them. With this in mind, we provide an introduction to these technologies and showcase how these have been used to gain an understanding of each of the major macromolecules that control the flow of information in normal and cancer cells: DNA, RNA, and Proteins. The first portion of the volume describes the use of microarrays and next generation sequencing for genome-wide analysis of genetic and epigenetic variation. The next portion provides an overview of these technolo-gies in the study of gene expression at the RNA level. The final section details the use of mass spectrometry and tissue microarrays for high-throughput and parallel analysis of proteins. As these technologies are deployed in cancer research, and the analytical approaches for interpretation of the resulting data mature, we will greatly increase our fundamental understanding of carcinogenesis and be able to translate this understanding for development of biomarkers and therapeutic strategies in the dawning era of individualized medicine.
Preface
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1 Genome-Scale Analysis of Data from High-Throughput Technologies ............................................................... 1Sarah J. Wheelan
2 Analysis of Inherited and Acquired Genetic Variation ......................... 13Srinivasan Yegnasubramanian and William B. Isaacs
3 Examining DNA–Protein Interactions with Genome-Wide Chromatin Immunoprecipitation Analysis ............................................. 33Esteban Ballestar and Manel Esteller
4 Genome-Wide DNA Methylation Analysis in Cancer Research ........... 47Srinivasan Yegnasubramanian and William G. Nelson
5 Use of Expression Microarrays in Cancer Research ............................. 67Jun Luo and Yidong Chen
6 Signal Sequencing for Gene Expression Profiling ................................. 87Biaoyang Lin, Jeremy Wechsler, and Leroy Hood
7 Mass Spectrometry Based Proteomics in Cancer Research .................. 117Mohamad A. Abbani, Parag Mallick, and Maryann S. Vogelsang
8 Tissue Microarrays in Cancer Research ................................................. 157Toby C. Cornish and Angelo M. De Marzo
Index ................................................................................................................. 185
Contents
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Mohamad AbbaniCedars-Sinai Medical Center, Los Angeles, CA, USA;Department of Chemistry and Biochemistry,University of California at Los Angeles,Los Angeles, CA, [email protected]
Esteban BallestarCancer Epigenetics Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain [email protected]
Yidong Chen National Cancer Institute, Bethesda, MD, USA [email protected]
Toby CornishDepartment of Pathology,Johns Hopkins University School of Medicine,Baltimore, MD, USA [email protected]
Angelo De MarzoDepartment of Pathology,Johns Hopkins University School of Medicine,Baltimore, MD, USA [email protected]
Manel Esteller Cancer Epigenetics Group,Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro 328029, Madrid, Spain [email protected]
Contributors
x Contributors
Leroy HoodInstitute for Systems Biology,Seattle, WA, [email protected]
William B. IsaacsSidney Kimmel Comprehensive Cancer Center,Brady Urological Institute,Johns Hopkins University School of Medicine,Baltimore, MD, [email protected]
Biaoyang LinDepartment of Urology, University of Washington, Seattle, WA, USA;Zhejiang-California International Nanosystems Institute, Hangzhou, China [email protected]
Jun LuoDepartment of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA [email protected]
Parag Mallick Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA, USA; Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA, USA [email protected]
William G. NelsonSidney Kimmel Comprehensive Cancer Center,Johns Hopkins University School of Medicine,Baltimore, MD, [email protected]
Maryann Vogelsang Cedars-Sinai Medical Center,Los Angeles, CA, USA;Department of Chemistry and Biochemistry,University of California at Los Angeles,Los Angeles, CA, [email protected]
xiContributors
Jeremy WechslerUniversity of Washington,Seattle, WA, USA
Sarah J. WheelanSidney Kimmel Comprehensive Cancer Center,Johns Hopkins University School of Medicine,Baltimore, MD, [email protected]
Srinivasan Yegnasubramanian Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA [email protected]
