(Methods in Molecular Biology 1015) Rosane Charlab, Lei Zhang (auth.), Federico Innocenti, Ron H.N. - Methods in Molecular Biology 1015 Federico

(Methods in Molecular Biology 1015) Rosane Charlab, Lei Zhang (auth.), Federico Innocenti, Ron H.N.

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Unformatted text preview: Methods in Molecular Biology 1015 Federico Innocenti Ron H. N. van Schaik Editors Pharmacogenomics Methods and Protocols Second Edition METHODS IN M O L E C U L A R B I O LO G Y ™ Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK For further volumes: Pharmacogenomics Methods and Protocols Second Edition Edited by Federico Innocenti Division of Pharmacotherapy and Experimental Therapeutics Lineberger Comprehensive Cancer Center, Institute for Pharmacogenomics and Individualized Therapy, Eshelman School of Pharmacy University of North Carolina, Chapel Hill, NC, USA Ron H.N. van Schaik Department of Clinical Chemistry (AKC), Erasmus University Medical Center Rotterdam, The Netherlands Editors Federico Innocenti Division of Pharmacotherapy and Experimental Therapeutics Lineberger Comprehensive Cancer Center Institute for Pharmacogenomics and Individualized Therapy Eshelman School of Pharmacy University of North Carolina Chapel Hill, NC, USA Ron H.N. van Schaik Department of Clinical Chemistry (AKC) Erasmus University Medical Center Rotterdam, The Netherlands ISSN 1064-3745 ISSN 1940-6029 (electronic) ISBN 978-1-62703-434-0 ISBN 978-1-62703-435-7 (eBook) DOI 10.1007/978-1-62703-435-7 Springer New York Heidelberg Dordrecht London Library of Congress Control Number: 2013938603 © Springer Science+Business Media, LLC 2013 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 Humana Press is a brand of Springer Springer is part of Springer Science+Business Media ( ) Preface Based upon the success of its first edition, the second edition of Pharmacogenomics: Methods and Protocols aims to continue to provide readers with high-quality content on the most innovative and commonly adopted technologies in the field of pharmacogenomics. Many contributors to this book are leading experts in this field. Pharmacogenomics: Methods and Protocols has become an established guide for investigators in the selection and the experimental application of pharmacogenomic technologies. Using the extensive information in the materials and methods sections, investigators will be able to easily perform each technique in their laboratories. This book is unique in that it identifies and highlights problems that might be encountered in performing a specific technique and how to overcome these. Each procedure is described in a stepwise fashion, providing detailed information from leading experts that is usually not found in research articles. Pharmacogenomics aims to study the genetic basis of interpatient variability in response to drug therapy. Understanding an individual’s genetic makeup is the key to creating personalized drugs with greater efficacy and safety. Various technologies are currently available, and this book aids the researchers’ decision on the most suitable method to apply. In this updated edition, an introductory chapter describes the history of pharmacogenomics and its current status. It is followed by Part II, which includes a variety of techniques that are currently available to interrogate a patient’s genome. Readers will find detailed information on eight technologies for SNP detection, plus three in-depth chapters on recent technological developments in epigenetic techniques, sequencing, and quality control. Relative to the first edition, newer methods such as SmartAmp, GoldenGate, and Luminex X MAP have now been included. Part III describes six methodologies and tools to assess and infer the functional significance of allele variation in humans, including more innovative in vitro models (assays to detect allelic imbalance or the effects of nonsynonymous variants and to guide identification of candidate genes) and in vivo assays in mice (use of genomically characterized inbred mice and the hydrodynamic tail vein assay for human promoters and enhancers). Part IV describes current tools for supporting the translation and implementation of pharmacogenomic markers in the clinic. Here, readers will find five completely new chapters on the latest repositories of pharmacogenomic information, a summary guide to the most recent Web-based resources of interest to pharmacogenomic researchers, and two key examples of algorithms and guidelines for treatment personalization based upon genetics. Pharmacologists, geneticists, molecular biologists, and physicians in academic institutions, in biotechnology, and in pharmaceutical industries will find Pharmacogenomics: Methods and Protocols, second edition an essential reference and a valuable source on the latest information in this field. v vi Preface We are extremely grateful to all the authors for their excellent contributions making this book a comprehensive and up-to-date resource for investigators in pharmacogenomics. Chapel Hill, NC, USA Rotterdam, The Netherlands Federico Innocenti Ron H.N. van Schaik Contents Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . PART I INTRODUCTION TO PHARMACOGENOMICS 1 Pharmacogenomics: Historical Perspective and Current Status. . . . . . . . . . . . . Rosane Charlab and Lei Zhang PART II v xi 3 TECHNIQUES FOR INTERROGATING VARIATION HUMAN GENES AND GENOMES IN 2 Denaturing High-Performance Liquid Chromatography for Mutation Detection and Genotyping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Donna Lee Fackenthal, Pei Xian Chen, Ted Howe, and Soma Das 3 Clinical SNP Detection by the SmartAmp Method . . . . . . . . . . . . . . . . . . . . . Toshihisa Ishikawa and Yoshihide Hayashizaki 4 MALDI-TOF Mass Spectrometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Dirk van den Boom, Matthias Wjst, and Robin E. Everts 5 TaqMan® Drug Metabolism Genotyping Assays for the Detection of Human Polymorphisms Involved in Drug Metabolism . . . . . . . . . . . . . . . . Toinette Hartshorne 6 Pyrosequencing of Clinically Relevant Polymorphisms . . . . . . . . . . . . . . . . . . . Cristi R. King and Sharon Marsh 7 Pharmacogenetics Using Luminex® xMAP® Technology: A Method for Developing a Custom Multiplex Single Nucleotide Polymorphism Mutation Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Gonnie Spierings and Sherry A. Dunbar 8 Use of Linkage Analysis, Genome-Wide Association Studies, and Next-Generation Sequencing in the Identification of Disease-Causing Mutations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Eric Londin, Priyanka Yadav, Saul Surrey, Larry J. Kricka, and Paolo Fortina 9 The GoldenGate Genotyping Assay: Custom Design, Processing, and Data Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Anna González-Neira vii 25 55 71 87 97 115 127 147 viii Contents 10 Genome-Wide Gene Expression Profiling, Genotyping, and Copy Number Analyses of Acute Myeloid Leukemia Using Affymetrix GeneChips. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mathijs A. Sanders and Peter J.M. Valk 11 Epigenetic Techniques in Pharmacogenetics . . . . . . . . . . . . . . . . . . . . . . . . . . Sandra G. Heil 12 Plasmid Derived External Quality Controls for Genetic Testing . . . . . . . . . . . . Tahar van der Straaten and Henk-Jan Guchelaar PART III 179 189 FUNCTIONAL ASSESSMENT OF GENETIC VARIATION: IN VITRO AND IN VIVO METHODS 13 Allelic Imbalance Assays to Quantify Allele-Specific Gene Expression and Transcription Factor Binding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Francesca Luca and Anna Di Rienzo 14 SCAN: A Systems Biology Approach to Pharmacogenomic Discovery . . . . . . . Eric R. Gamazon, R. Stephanie Huang, and Nancy J. Cox 15 Methods to Examine the Impact of Nonsynonymous SNPs on Protein Degradation and Function of Human ABC Transporter . . . . . . . . . Toshihisa Ishikawa, Kanako Wakabayashi-Nakao, and Hiroshi Nakagawa 16 In Vitro Identification of Cytochrome P450 Enzymes Responsible for Drug Metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zhengyin Yan and Gary W. Caldwell 17 In Vitro and In Vivo Mouse Models for Pharmacogenetic Studies . . . . . . . . . . Amber Frick, Oscar Suzuki, Natasha Butz, Emmanuel Chan, and Tim Wiltshire 18 The Hydrodynamic Tail Vein Assay as a Tool for the Study of Liver Promoters and Enhancers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mee J. Kim and Nadav Ahituv PART IV 155 201 213 225 251 263 279 TOOLS FOR TRANSLATION AND IMPLEMENTATION PHARMACOGENETIC MARKERS OF 19 A Guide to the Current Web-Based Resources in Pharmacogenomics . . . . . . . Dylan M. Glubb, Steven W. Paugh, Ron H.N. van Schaik, and Federico Innocenti 20 PharmGKB: The Pharmacogenomics Knowledge Base . . . . . . . . . . . . . . . . . . Caroline F. Thorn, Teri E. Klein, and Russ B. Altman 21 Genetic Databases in Pharmacogenomics: The Frequency of Inherited Disorders Database (FINDbase). . . . . . . . . . . . . . Marianthi Georgitsi and George P. Patrinos 293 311 321 Contents 22 Development of Predictive Models for Estimating Warfarin Maintenance Dose Based on Genetic and Clinical Factors . . . . . . . . . . . . . . . . Lu Yang and Mark W. Linder 23 Evidence Based Drug Dosing and Pharmacotherapeutic Recommendations per Genotype. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Vera H.M. Deneer and Ron H.N. van Schaik Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix 337 345 355 Contributors NADAV AHITUV • Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, University of California, San Francisco, CA, USA RUSS B. ALTMAN • Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA NATASHA BUTZ • Division of Pharmacotherapy and Experimental Therapeutics, Institute for Pharmacogenomics and Individualized Therapy, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA GARY W. CALDWELL • CREATe, Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, PA, USA EMMANUEL CHAN • Division of Pharmacotherapy and Experimental Therapeutics, Institute for Pharmacogenomics and Individualized Therapy, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA ROSANE CHARLAB • Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA PEI XIAN CHEN • Department of Human Genetics, University of Chicago, Chicago, IL, USA NANCY J. COX • Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA SOMA DAS • Department of Human Genetics, University of Chicago, Chicago, IL, USA ANNA DI RIENZO • Department of Human Genetics, University of Chicago, Chicago, IL, USA VERA H.M. DENEER • Department of Clinical Pharmacy, St. Antonius Ziekenhuis Nieuwegein, Nieuwegein, The Netherlands SHERRY A. DUNBAR • Luminex Corporation, Austin, TX, USA ROBIN E. EVERTS • SEQUENOM® Inc., San Diego, CA, USA DONNA LEE FACKENTHAL • Department of Human Genetics, University of Chicago, Chicago, IL, USA PAOLO FORTINA • Cancer Genomics Laboratory, Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Jefferson Medical College, Philadelphia, PA, USA AMBER FRICK • Division of Pharmacotherapy and Experimental Therapeutics, Institute for Pharmacogenomics and Individualized Therapy, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA ERIC R. GAMAZON • Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA MARIANTHI GEORGITSI • Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece DYLAN M. GLUBB • Queensland Institute of Medical Research, Brisbane, QLD, Australia ANNA GONZÁLEZ-NEIRA • Human Genotyping Unit, Spanish National Cancer Research Center (CNIO), Madrid, Spain xi xii Contributors HENK-JAN GUCHELAAR • Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands TOINETTE HARTSHORNE • Life Technologies, South San Francisco, CA, USA YOSHIHIDE HAYASHIZAKI • Preventive Medicine and Diagnosis Innovation Program, RIKEN, Wako, Japan SANDRA G. HEIL • Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands TED HOWE • Transgenomic Inc., Omaha, NE, USA R. STEPHANIE HUANG • Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA FEDERICO INNOCENTI • Division of Pharmacotherapy and Experimental Therapeutics, Lineberger Comprehensive Cancer Center, Institute for Pharmacogenomics and Individualized Therapy, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA TOSHIHISA ISHIKAWA • Center for Life Science Technologies, RIKEN, Yokohama, Japan MEE J. KIM • Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, University of California, San Francisco, CA, USA CRISTI R. KING • Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO, USA TERI E. KLEIN • Department of Genetics, Stanford University Medical Center, Stanford, CA, USA LARRY J. KRICKA • Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA MARK W. LINDER • Department of Pathology and Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY, USA ERIC LONDIN • Computational Medicine Center, Thomas Jefferson University Jefferson Medical College, Philadelphia, PA, USA FRANCESCA LUCA • Department of Human Genetics, University of Chicago, Chicago, IL, USA SHARON MARSH • Faculty of Pharmacy and Pharmaceutical Sciences, Katz Group Centre for Pharmacy and Health Research, University of Alberta, Edmonton, AB, Canada HIROSHI NAKAGAWA • College of Bioscience and Biotechnology, Chubu University, Aichi, Japan GEORGE P. PATRINOS • Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece STEVEN W. PAUGH • Hematological Malignancies Program and Pharmaceutical Sciences Department, St. Jude Children’s Research Hospital, Memphis, TN, USA MATHIJS A. SANDERS • Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands GONNIE SPIERINGS • Luminex B.V., Oosterhout, The Netherlands SAUL SURREY • Department of Medicine, Thomas Jefferson University, Jefferson Medical College, Philadelphia, PA, USA OSCAR SUZUKI • Division of Pharmacotherapy and Experimental Therapeutics, Institute for Pharmacogenomics and Individualized Therapy, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA CAROLINE F. THORN • Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA Contributors PETER J.M. VALK • Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands RON H.N. VAN SCHAIK • Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands DIRK VAN DEN BOOM • SEQUENOM® Inc., San Diego, CA, USA TAHAR VAN DER STRAATEN • Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands KANAKO WAKABAYASHI-NAKAO • Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan TIM WILTSHIRE • Division of Pharmacotherapy and Experimental Therapeutics, Institute for Pharmacogenomics and Individualized Therapy, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA MATTHIAS WJST • Comprehensive Pneumology Center (CPC), Helmholtz Zentrum Muenchen, German Research Center for Environmental Health (GmbH), Neuherberg, Germany; Institute of Medical Statistics and Epidemiology, Klinikum Rechts der Isar der TU Muenchen, Muenchen, Germany PRIYANKA YADAV • Cancer Genomics Laboratory, Kimmel Cancer Center, Thomas Jefferson University, Jefferson Medical College, Philadelphia, PA, USA ZHENGYIN YAN • CREATe, Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, PA, USA LU YANG • Department of Pathology and Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY, USA LEI ZHANG • Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA xiii Part I Introduction to Pharmacogenomics Chapter 1 Pharmacogenomics: Historical Perspective and Current Status Rosane Charlab and Lei Zhang Abstract Pharmacogenomics and its predecessor pharmacogenetics study the contribution of genetic factors to the interindividual variability in drug efficacy and safety. One of the major goals of pharmacogenomics is to tailor drugs to individuals based on their genetic makeup and molecular profile. From early findings in the 1950s uncovering inherited deficiencies in drug metabolism that explained drug-related adverse events, to nowadays genome-wide approaches assessing genetic variation in multiple genes, pharmacogenomics has come a long way. The evolution of pharmacogenomics has paralleled the evolution of genotyping technologies, the completion of the human genome sequencing and the HapMap project. Despite these advances, the implementation of pharmacogenomics in clinical practice has yet been limited. Here we present an overview of the history and current applications of pharmacogenomics in patient selection, dosing, and drug development with illustrative examples of these categories. Some of the challenges in the field and future perspectives are also presented. Key words Pharmacogenetics, Pharmacogenomics, Pharmacokinetics, Pharmacodynamics, Polymorphism, Adverse event, Targeted therapy, Drug metabolizing enzyme, Drug transporter 1 Pharmacogenomics: Historical Perspective and Current Status It is well known that people respond differently to medications. The same medication can be well tolerated and/or effectiv...
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