GENETIC ASSOCIATION STUDIES: Background, Conduct, Analysis, Interpretation This page intentionally left blank GENETIC ASSOCIATION STUDIES: Background, Conduct, Analysis, Interpretation Mehmet Tevfik Dorak Vice President: Denise Schanck Senior Editor: Elizabeth Owen Assistant Editor: David Borrowdale Production Editor: Deepa Divakaran Illustrator: Oxford Designers & Illustrators Ltd Layout: Nova Techset Ltd Cover Designer: AM Design Copyeditor: Jo Clayton Proofreader: Susan Wood Indexer: Bill Johncocks ©2017 by Garland Science, Taylor & Francis Group, LLC This book contains information obtained from authentic and highly regarded sources. Every effort has been made to trace copyright holders and to obtain their permission for the use of copyright material. Reprinted material is quoted with permission, and sources are indicated. A wide variety of references are listed. Reasonable efforts have been made to publish reliable data and information, but the author and the publisher cannot assume responsibility for the validity of all materials or for the consequences of their use. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means—graphic, electronic, or mechanical, including photocopying, recording, taping, or information storage and retrieval systems— without permission of the copyright holder. ISBN 978-0-8153-4463-6 Library of Congress Cataloging-in-Publication Data Names: Dorak, M. Tevfik, author. Title: Genetic association studies : background, conduct, analysis, interpretation / Mehmet Tevfik Dorak. Description: New York, NY : Garland Science, Taylor & Francis Group, LLC, [2017] | Includes bibliographical references. Identifiers: LCCN 2016030624 | ISBN 9780815344636 (alk. paper) Subjects: | MESH: Genetic Association Studies | Genetic Phenomena | Molecular Epidemiology--methods Classification: LCC QH437 | NLM QU 550 | DDC 576.5--dc23 LC record available at https://lccn.loc.gov/2016030624 Published by Garland Science, Taylor & Francis Group, LLC, an informa business, 711 Third Avenue, New York, NY, 10017, USA, and 2 Park Square, Milton Park, Abingdon, OX14 4RN, UK. Printed in the United Kingdom 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 Visit our website www.garlandscience.com Preface This book has been written at probably the most challenging and exciting time in the recent history of genetics. The last decade has seen the completion of one revolutionary project after another, such as the ENCODE and NIH Roadmap Epigenomics projects. Both of these required the rewriting of a large proportion of the text, and the recent develop- ments in translational bioinformatics forced the addition of a new chapter. Genetic Association Studies brings together in one place the most relevant aspects of genetics, environmental and genetic epidemiology, and statistics. Laboratory aspects of genetic association studies are also included. Although genome-wide association studies have changed the way we think about genetic associations, candidate gene studies and more basic genotyping methods are included to make sure that the book is relevant to students and researchers with limited resources. I hope every reader interested in genetic associa- tions will find something useful here, and especially that students will benefit from having a single source covering different features of genetic associations. The book does not claim to be a comprehensive monograph on genetic epidemiology, but rather demystifies key concepts for those who have not received formal training in epidemiology or statistics. Writing this book has felt at times like chasing a moving target, and sometimes I wondered how it was going to be possible to finish. It wouldn’t have been possible without the under- standing, encouragement, and tenacity of the staff at Garland Science, especially Liz Owen and David Borrowdale. A book incorporating information from different disciplines and written as a solo effort is bound to have imperfections. Expert reviewers worked very hard to help to improve the quality of information contained in the text. I am very much grate- ful to all reviewers. Any remaining errors are my responsibility. I must also thank my stu- dents, who have seen many different versions of this book and provided a lot of feedback, both knowingly and unknowingly. In particular, I am most grateful to my former graduate students, Amy E. Kennedy and Sandeep K. Singh, for their tireless efforts. My wife Chris- tina suffered more than her fair share while I was trying to finish the book and I thank her for never-ending support and her encouragement in bringing this project to successful completion. Finally, I must express my gratitude to everyone who has contributed to my development, especially my family, teachers, mentors, and colleagues. Mehmet Tevfik Dorak This page intentionally left blank Acknowledgments The author and publisher would like to thank external advisers and reviewers for their suggestions and advice in preparing the text and figures. Jennifer Barrett, University of Leeds, UK; Farren Briggs, Case Western Reserve University, USA; Corinne D. Engelman, University of Wisconsin, USA; Amy Kennedy, National Cancer Institute, USA; Christine Ladd-Acosta, Johns Hopkins Bloomberg School of Public Health, USA; Caroline Relton, Newcastle University, UK; Michael Routledge, University of Leeds, UK; James Tang, University of Alabama at Birmingham, USA; Dawn Teare, University of Sheffield, UK; Timothy Thornton, University of Washington, USA; Joe Wiemels, University of California, San Francisco, USA; Maurice Zeegers, University of Birmingham, UK. This page intentionally left blank Contents Preface v 6.2 Study Design and Errors 93 6.3 Data Analysis 98 Acknowledgments vii 7 Genotyping Methods and Errors 105 1 Primer on Molecular Genetics 1 7.1 Genotyping Principles 105 1.1 Genetic Variation 1 7.2 Genotyping and PCR 105 1.2 The Human Genome 13 7.3 Choice of Genotyping Method 110 1.3 Consequences of Genetic Variation 17 7.4 Sources of DNA for Genotyping 113 1.4 Genetic Nomenclature 22 7.5 Genotyping Errors 114 2 Primer on Medical Genetics 25 7.6 Imputing Genotypes 119 2.1 The Location of Disease-causing Mutations 25 8 Candidate Gene Studies and 2.2 Single-Gene, Oligogenic, and Multigenic Genome-Wide Association Studies 123 Disorders 28 8.1 Candidate Genes 123 2.3 Copy Number of Mutant Genes 32 8.2 C andidate Variants 125 2.4 Inherited Mutations 35 8.3 Candidate Gene Studies in the GWAS age 130 3 Primer on Population Genetics 41 8.4 Advantages and Disadvantages of a GWAS 132 3.1 Hardy–Weinberg Equilibrium 41 9 Statistical Analysis of Genetic 3.2 Linkage Disequilibrium 45 Association Study Results 139 3.3 Population Substructure 52 9.1 Standard Genetic Association Analysis 139 3.4 Signatures of Natural Selection 54 9.2 GWAS Analysis 152 4 Epidemiologic Principles and 10 Bioinformatics for the Interpretation Genetic Association Studies 57 of Genetic Association Study 4.1 Types of Epidemiologic Association Studies 57 Results 163 4.2 Chance, Bias, Confounding, and Effect 10.1 Bioinformatics for Testing SNP Associations 163 Modification 64 10.2 Functional Annotation of SNPs 168 4.3 Causality and Statistical Association 71 10.3 Analyzing Functionally Altered Genes 181 5 Environmental Epidemiology in the Context of Genetic Epidemiology 75 11 Genetic Risk Profiling and Medical 5.1 Studying Environmental Effects 76 Applications of Genetic Associations 187 5.2 Examining and Estimating Environmental 11.1 Genetic Risk Profiling and Genetic Markers 187 Effects 78 11.2 Assessing Clinical Utility 192 5.3 The Environment and Gene Activity 83 11.3 Disease Biology and Pharmacogenomics 196 5.4 Gene and Environment Interactions, Personalized Prevention, and Treatment 84 Glossary 201 Index 219 6 Elementary Statistical Concepts 89 6.1 Statistical Power and Statistical Significance 90