Cancer Susceptibility: Methods and Protocols PDF
Preview Cancer Susceptibility: Methods and Protocols
M M B ™ ethods in olecular iology Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK For other titles published in this series, go to www.springer.com/series/7651 Cancer Susceptibility Methods and Protocols Edited by Michelle Webb Faculty of Medical and Human Sciences, School of Clinical Laboratory Sciences, University of Manchester, Manchester, UK Editor Michelle Webb, Ph.D. Faculty of Medical and Human Sciences School of Clinical Laboratory Sciences University of Manchester, Manchester, UK [email protected] ISSN 1064-3745 e -ISSN 1940-6029 ISBN 978-1-60761-758-7 e-ISBN 978-1-60761-759-4 DOI 10.1007/978-1-60761-759-4 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2010930786 © Springer Science+Business Media, LLC 2010 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Humana Press, c/o 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 connection 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. While the advice and information in this book are believed to be true and accurate at the date of going to press, 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. Cover Illustration Caption: Figure 1 from Chapter 3. Printed on acid-free paper Humana Press is a part of Springer Science+Business Media (www.springer.com) Preface Over the past 2 decades, spectacular advances have been made in understanding the molecular genetics of cancer. One of the major objectives of modern day cancer research is to identify genes that when mutated result in an increased susceptibility to the disease. This knowledge can be translated into clinical practice where screening for a predisposi- tion becomes part of an at-risk patient’s surveillance and management strategy. An exam- ple where this has been successful is in the management of hereditary breast cancer. Following the identification of the breast cancer susceptibility genes, BRCA1 and BRCA2, in the early 1990s, genetic screens that estimate a patient’s risk have now become avail- able. While this success is now being extended to other cancer disorders, more genes need to be identified, characterized, and screens need to be developed. A book that brings together the most recent technological developments for identifying and screening cancer susceptibility genes is therefore very timely. The book is separated broadly into two parts. The first part, gene identification, informs scientists working at identifying novel cancer susceptibility genes, while the second part deals with mutation screening technologies that aid scientists and clinicians working to translate this knowledge into the clinic. Manchester, UK Michelle Webb v Contents Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix Part I IdentIfyIng CanCer SuSCePtIbIlIty geneS 1 The Identification of Colon Cancer Susceptibility Genes by Using Genome-Wide Scans .................................. 3 Denise Daley 2 Prioritizing Candidate Genetic Modifiers of BRCA1 and BRCA2 Using a Combinatorial Analysis of Global Expression and Polymorphism Association Studies of Breast Cancer ....................... 23 Logan C. Walker and Amanda B. Spurdle 3 Microarray-Based Comparative Genomic Hybridization (Array-CGH) as a Useful Tool for Identifying Genes Involved in Glioblastoma (GB).............................................. 35 Yolanda Ruano, Manuela Mollejo, Angel Rodríguez de Lope, José Luis Hernández-Moneo, Pedro Martínez, and Bárbara Meléndez 4 Multiplex Amplifiable Probe Hybridization (MAPH) Methodology as an Alternative to Comparative Genomic Hybridization (CGH)............. 47 Ludmila Kousoulidou, Carolina Sismani, and Philippos C. Patsalis 5 Utilizing Saccharomyces Cerevisiae to Identify Aneuploidy and Cancer Susceptibility Genes............................. 73 Erin D. Strome and Sharon E. Plon 6 Computational Identification of Cancer Susceptibility Loci.................. 87 Marko Laakso, Sirkku Karinen, Rainer Lehtonen, and Sampsa Hautaniemi 7 Digital Candidate Gene Approach (DigiCGA) for Identification of Cancer Genes ....................................... 105 Meng-Jin Zhu, Xiang Li, and Shu-Hong Zhao Part II SCreenIng CanCer SuSCePtIbIlIty geneS 8 The Use of Denaturing High Performance Liquid Chromatography (DHPLC) for Mutation Scanning of Hereditary Cancer Genes............... 133 Deborah J. Marsh and Viive M. Howell 9 Enhanced Mismatch Mutation Analysis: Simultaneous Detection of Point Mutations and Large Scale Rearrangements by Capillary Electrophoresis, Application to BRCA1 and BRCA2 ...................... 147 Claude Houdayer, Virginie Moncoutier, Jérôme Champ, Jérémie Weber, Jean-Louis Viovy, and Dominique Stoppa-Lyonnet vii viii Contents 10 Economical Protocol for Combined Single-Strand Conformation Polymorphism and Heteroduplex Analysis on a Standard Capillary Electrophoresis Apparatus........................................... 181 Piotr Kozlowski and Wlodzimierz J. Krzyzosiak 11 Mutational Screening of hMLH1 and hMSH2 that Confer Inherited Colorectal Cancer Susceptibility Using Denature Gradient Gel Electrophoresis (DGGE) ........................................... 193 Tao Liu 12 s-RT-MELT: A Novel Technology for Mutation Screening.................. 207 Jin Li and G. Mike Makrigiorgos 13 Zoom-In Array Comparative Genomic Hybridization (aCGH) to Detect Germline Rearrangements in Cancer Susceptibility Genes ........... 221 Johan Staaf and Åke Borg 14 Development of a Scoring System to Screen for BRCA1/2 Mutations.......... 237 Gareth R. Evans and Fiona Lalloo 15 Use of Splicing Reporter Minigene Assay to Evaluate the Effect on Splicing of Unclassified Genetic Variants ..................... 249 Pascaline Gaildrat, Audrey Killian, Alexandra Martins, Isabelle Tournier, Thierry Frébourg, and Mario Tosi 16 Functional Analysis of Human BRCA2 Variants Using a Mouse Embryonic Stem Cell-Based Assay ............................. 259 Sergey G. Kuznetsov, Suhwan Chang, and Shyam K. Sharan 17 Developing Functional Assays for BRCA1 Unclassified Variants .............. 281 Michelle Webb Index.............................................................. 293 Contributors Åke borg • Department of Oncology, Clinical Sciences, CREATE Health Strategic Centre For Translational Cancer Research, Lund University, Lund, Sweden Jérôme ChamP • Service de Génétique Oncologique, Institut Curie Hôpital, Paris, France Suhwan Chang • Center for Cancer Research, Mouse Cancer Genetics Program, National Cancer Institute at Frederick, Frederick, MD, USA denISe daley • Department of Medicine, St . Paul’s Hospital, University of British Columbia, Vancouver, BC, Canada gareth r. evanS • Medical Genetics Research Group and Regional Genetics Service, St Mary’s Hospital, University of Manchester and Central Manchester and Manchester Children’s University Hospitals NHS Trust, Manchester, UK thIerry frébourg • Faculty of Medicine Department of Genetics and Institute for Biomedical Research, Rouen University Hospital, Inserm U614, IFRMP, University of Rouen, Northwest Canceropole, Rouen, France PaSCalIne gaIldrat • Faculty of Medicine Department of Genetics and Institute for Biomedical Research, Rouen University Hospital, Inserm U614, IFRMP, University of Rouen, Northwest Canceropole, Rouen, France SamPSa hautanIemI • Computational Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland JoSé luIS hernández-moneo • Department of Neurosurgery, Virgen de la Salud Hospital, Toledo, Spain Claude houdayer • Service de Génétique Oncologique, Institut Curie Hôpital, Paris, France; Faculté de Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, Paris, France vIIve m. howell • Royal North Shore Hospital, Kolling Institute of Medical Research, University of Sydney, Sydney, NSW, Australia SIrkku karInen • Computational Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland audrey kIllIan • Faculty of Medicine Department of Genetics and Institute for Biomedical Research, Rouen University Hospital, Inserm U614, IFRMP, University of Rouen, Northwest Canceropole, Rouen, France ludmIla kouSoulIdou • Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus PIotr kozlowSkI • Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland wlodzImIerz J. krzyzoSIak • Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland ix x Contributors Sergey g. kuznetSov • Center for Cancer Research, Mouse Cancer Genetics Program, National Cancer Institute at Frederick, Frederick, MD, USA; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland marko laakSo • Computational Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland fIona lalloo • Medical Genetics Research Group and Regional Genetics Service, St Mary’s Hospital, University of Manchester and Central Manchester and Manchester Children’s University Hospitals NHS Trust, Manchester, UK raIner lehtonen • Department of Biological and Environmental Sciences, Metapopulation Research Group, University of Helsinki, Helsinki, Finland JIn lI • Division of Genomic Stability and Division of DNA Repair and Medical Physics and Biophysics, Department of Radiation Oncology, Harvard Medical School, Dana Farber Cancer Institute and Brigham and Women’s Hospital, Boston, MA, USA XIang lI • Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China tao lIu • Cancer Centre Karolinska, Karolinska Institute, Stockholm, Sweden g. mIke makrIgIorgoS • Division of Genomic Stability and Division of DNA Repair and Medical Physics and Biophysics, Department of Radiation Oncology, Harvard Medical School, Dana Farber Cancer Institute and Brigham and Women’s Hospital, BostonMA, USA deborah J. marSh • Royal North Shore Hospital, Kolling Institute of Medical Research, University of Sydney, Sydney,NSW, Australia Pedro martínez • Department of Genetics, Virgen de la Salud Hospital, Toledo, Spain aleXandra martInS • Faculty of MedicineDepartment of Genetics and Institute for Biomedical Research, Rouen University Hospital, Inserm U614, IFRMP, University of Rouen, Northwest Canceropole, Rouen, France bárbara meléndez • Molecular Pathology Research Unit, Virgen de la Salud Hospital, Toledo, Spain manuela molleJo • Department of Pathology and Molecular Pathology Research Unit, Virgen de la Salud Hospital, Toledo, Spain vIrgInIe monCoutIer • Service de Génétique Oncologique, Institut Curie Hôpital, Paris, France PhIlIPPoS C. PatSalIS • Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus Sharon e. Plon • Department of Molecular and Human Genetics, Baylor College of Medicine, Houston,TX, USA angel rodríguez de loPe • Department of Neurosurgery, Virgen de la Salud Hospital, Toledo, Spain yolanda ruano • Molecular Pathology Research Unit, Virgen de la Salud Hospital, Toledo, Spain
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