Human Genome Epidemiology (2nd ed.): Building the evidence for using genetic information to improve health and prevent disease
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Human Genome Epidemiology 2nd edition book cover
Copyright
New York Oxford
OXFORD UNIVERSITY PRESS
2010
Oxford University Press
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Materials appearing in this book prepared by individuals as part of their official duties as United States government employees are not covered by the above-mentioned copyright, and any views expressed therein do not necessarily represent the views of the United States government. Such individuals’ participation in the Work is not meant to serve as an official endorsement of any statement to the extent that such statement may conflict with any official position of the United States government. Top of Page
Preface
In the first edition of Human Genome Epidemiology published in 2004, we discussed how the epidemiologic approach provides an important scientific foundation for studying the continuum from gene discovery to the development, applications, and evaluation of human genome information in improving health and preventing disease. Since 2004, advances in human genomics have continued to occur at a breathtaking pace. Although the concept of personalized healthcare and disease prevention often promised by enthusiastic scientists and the media is yet to be fulfilled, we are now seeing progress and rapid accumulation of data in many “omics” related research fields. New methods to measure genome variation on an unprecedented large scale have propelled a new generation of genome-wide association studies. Evaluation of rare variants and full sequencing at large-scale are rapidly becoming a reality. Also, we have seen the emergence of population-based biobanks in many countries with the objectives of quantifying longitudinally the joint influences of genetic and environmental factors on the occurrence of common diseases.
With all these ongoing developments, we have invited many authors who are leaders in the field to produce the second edition of Human Genome Epidemiology. Our aim is to inform readers of new developments in the genomics field and how epidemiologic methods are being used to make sense of this information. We do realize that the material presented in this book will be outdated even before it is published. However, the methodologic challenges and possible solutions to them will remain with us for quite some time. There is very little material remaining from the first edition of Human Genome Epidemiology.
This new edition is divided into five parts. In Part I, we revisit the fundamentals of human genome epidemiology. We first give an overview of the development and progress in applications of genomic technologies with a focus on genomic sequence variation (Chapter 2). We then give an overview of the multidisciplinary field of public health genomics that includes a fundamental role of epidemiologic methods and approaches (Chapter 3). We also present a brief overview of evolving methods for tracking and compiling information on genetic factors in disease (Chapter 4).
In Part II, we discuss methodologic developments in collection, analysis, and synthesis of data from human genome epidemiologic studies. We discuss the emergence of biobanks around the world (Chapter 5), the evolution of case-control studies and cohort studies in the era of GWAS (Chapter 6), and the emerging role of consortia and networks (Chapter 7). Next, we discuss methodologic analytic issues in GWAS (Chapter 8) and the analytic challenges of gene-gene and gene-environment interaction (Chapter 9). We then address issues of reporting of genetic associations (Chapter 10), evolving methods for integrating the evidence (Chapter 11) as well as assessment of cumulative evidence and field synopses (Chapter 12).
In Part III, we provide several case studies that attempt to present an evolving knowledge base of the cumulative evidence on genetic variation in a variety of human diseases. As the information undoubtedly will change (even before the publication of the book), we stress here the importance of strong methodologic foundation for analysis and synthesis of information from various studies. The diseases shown in this section include three cancers: colorectal cancer (Chapter 13), childhood leukemia (Chapter 14), and bladder cancer (Chapter 15). We also present data from type 2 diabetes (Chapter 16), osteoporosis (Chapter 17), preterm birth (Chapter 18), coronary heart disease (Chapter 19), and schizophrenia (Chapter 20). Collectively, these chapters cover an impressive array of common complex human diseases and provide an epidemiologic approach to rapidly emerging data on gene-disease and gene-environment interactions.
In Part IV, we discuss methodologic issues surrounding specific applications of human genomic information for medicine and public health. We start in Chapter 21 with a review of the concept of Mendelian Randomization, an approach that allows us to assess the role of environmental factors and other biomarkers in the occurrence of human diseases using data on the association of genetic variation and disease endpoints. In Chapter 22, we discuss how clinical epidemiologic concepts and methods can be used to assess whether or not one or more genetic variants (e.g., genome profiles) can be used to predict risk for human diseases. Chapter 23 presents a major milestone for public health genomics, namely the publication of methods of systematic review and assessment of the clinical validity and utility of genomic applications in clinical practice. This chapter is a reprint of the published paper from the independent multidisciplinary panel, the EGAPP™ working group, supported by CDC and many partners. Chapter 24 briefly summarizes how reviews of the evidence on validity and utility of genomic information can be done systematically and rapidly, even in the face of incomplete information. Chapter 25 focuses on the crucial role of the behavioral and social sciences in assessing the impact and value of epidemiologic information on gene-disease associations. Chapter 26 addresses issues in evaluating developments in newborn screening. Chapter 27 provides an epidemiologic framework for the evaluation of pharmacogenomic applications in clinical and public health practice. Chapter 28 presents an overview of the relevance and impact of epigenomics in clinical practice and disease prevention. Finally, Chapter 29 presents an epidemiologic framework for evaluating family health history as a tool for disease prevention and health promotion. Even in this genomics era, family history remains a strong foundation, not only for identifying single gene disorders, but also for stratifying individuals and populations by different levels of disease risk and implementing personalized interventions.
Finally, in Part V of the book, we present a few case studies of the application of epidemiologic methods of assessment of clinical validity and utility for several disease examples. These include two pharmacogenomic testing examples—initial treatment of depression with SSRIs (Chapter 30) and warfarin therapy (Chapter 31). We also present information on population screening for hereditary hemochromatosis (Chapter 32), a genetic disorder with incomplete penetrance that has attracted some attention over the past decade as a possible example of population screening in the genomics era.
The second edition of Human Genome Epidemiology is primarily targeted to basic, clinical, and population scientists involved in studying genetic factors in common diseases. In addition, the book focuses on practical applications of human genome variation in clinical practice and disease prevention. We hope that students, clinicians, public health professionals, and policy makers will find the book useful in learning about evolving epidemiologic methods for approaching the discovery and the use of genetic information in medicine and public health in the twenty-first century.
Atlanta MJK, SB, MG
Cambridge JH
Ioannina JI
Ottawa JL
2009 Top of Page
Acknowledgments
We are grateful to the following individuals for reviewing drafts of selected book chapters:
- Louise Acheson
- Betsy Anagnostelis
- Melissa Austin
- Wylie Burke
- Melinda Clyne
- Rajvir Dahiya
- W. David Dotson
- Michael P. Douglas
- Nicole Dowling
- Jennifer L. Flome
- Sara Giordano
- Ridgely Fisk Green
- Scott Grosse
- Daurice A. Grossniklaus
- Idris Guessous
- Jennifer Harris
- Steve Hawken
- Terri Jackson
- Candice Y. Johnson
- Fontini Kavvoura
- Katherine Kolor
- Ruth Loos Denise Lowe
- Stephanie Melillo
- Melanie Myers
- Renée M. Ned
- Nikolaos Patsopoulos
- Paul Pharoah
- Margaret Piper
- Beth Potter
- Jessica L. Rowell
- Simon Sanderson
- Linda Sharp
- Camilla Stoltenberg
- John Thompson
- Rodolfo Valdez
- Jan Vandenbroucke
- David Veenstra
- Bridget Wilcken
- Lauren E. Williams
- Quanhe Yang
- Ajay Yesupriya
- Wei Yu
Table of Contents
Part I – Fundamentals of Human Genome Epidemiology Revisited
-
Human genome epidemiology: The road map revisited
Muin J. Khoury, Sara R. Bedrosian, Marta L. Gwinn, Julian P. T. Higgins, John P. A. Ioannidis, and Julian Little - Principles of analysis of germline genetics
Jesus Gonzalez-Bosquet and Stephen J. Chanock - The public health genomics enterprise
Philippa Brice and Ron Zimmern -
Navigating the evolving knowledge of human genetic variation in health and disease
Marta L. Gwinn and Wei Yu
Part II – Methods and Approaches for Data Collection, Analysis, and Integration
- The global emergence of epidemiological biobanks: Opportunities and challenges
Paul R. Burton, Isabel Fortier, and Bartha Knoppers - Case-control and cohort studies in the age of genome-wide associations
Teri Manolio -
The emergence of networks in human genome epidemiology: Challenges and opportunities
Daniela Seminara, Muin J. Khoury, Thomas R. O’Brien, Teri Manolio, Marta L. Gwinn, Julian Little, Julian P. T. Higgins, Jonine L. Bernstein, Paolo Boffetta, Melissa L. Bondy, Molly S. Bray, Paul E. Brenchley, Patricia A. Buffler, Juan Pablo Casas, Anand P. Chokkalingam, John Danesh, George Davey-Smith, Siobhan M. Dolan, Ross Duncan, Nelleke A. Gruis, Mia Hashibe, David J. Hunter, Marjo-Riitta Jarvelin, Beatrice Malmer, Demetrius M. Maraganore, Julia A. Newton-Bishop, Elio Riboli, Georgia Salanti, Emanuela Taioli, Nic Timpson, Andre´ G. Uitterlinden, Paolo Vineis, Nick Wareham, Deborah M. Winn, Ron Zimmern, and John P. A. Ioannidis - Design and analysis issues in genome-wide association studies
Duncan C. Thomas - The challenge of assessing complex gene–gene and gene–environment interactions
Peter Kraft and David J. Hunter -
STrengthening the REporting of Genetic Association Studies (STREGA)—An extension of the STROBE statement
Julian Little, Julian P.T. Higgins, John P.A. Ioannidis, David Moher, France Gagnon, Erik von Elm, Muin J. Khoury, Barbara Cohen, George Davey-Smith, Jeremy Grimshaw, Paul Scheet, Marta L. Gwinn, Robin E. Williamson, Guang Yong Zou, Kimberley Hutchings, Candice Y. Johnson, Valerie Tait, Miriam Wiens, Jean Golding, Cornelia van Duijn, John McLaughlin, Andrew Paterson, George Wells, Isabel Fortier, Matthew Freedman, Maja Zecevic, Richard A King, Claire Infante-Rivard, Alexandre Stewart, and Nick Birkett - Integration of the evidence on gene-disease associations: Methods of HuGE reviews
Julian P.T. Higgins and Julian Little -
Genome-wide association studies, field synopses, and the development of the knowledge base on genetic variation and human disease
Muin J. Khoury, Lars Bertram, Paolo Boffetta, Adam S. Butterworth, Stephen J. Chanock, Siobhan M. Dolan, Isabel Fortier, Montserrat Garcia-Closas, Marta L. Gwinn, Julian P. T. Higgins, A. Cecile J.W. Janssens, James M. Ostell, Ryan P. Owen, Roberta A. Pagon, Timothy R. Rebbeck, Nathaniel Rothman, Jonine L. Bernstein , Paul R. Burton, Harry Campbell, Anand P. Chokkalingam, Helena Furberg, Julian Little, Thomas R. O’Brien, Daniela Seminara, Paolo Vineis, Deborah M. Winn, Wei Yu, and John P.A. Ioannidis
PART III – Case Studies: Cumulative Assessment of the Role of Human Genome Variation in Specific Diseases
-
Colorectal cancer
Harry Campbell, Steven Hawken, Evropi Theodoratou, Alex Demarsh, Kimberley Hutchings, Candice Y. Johnson, Lindsey Masson, Linda Sharp, Valerie Tait, and Julian Little - Childhood leukemias
Anand P. Chokkalingam and Patricia A. Buffler - Bladder cancer
Jonine D. Figueroa, Montserrat Garcia-Closas, and Nathaniel Rothman - Type 2 diabetes
Eleftheria Zeggini and Mark I. McCarthy - Osteoporosis
André G. Uitterlinden, Joyce B.J. van Meurs, and Fernando Rivadeneira - Preterm birth
Siobhan M. Dolan - Coronary heart disease
Adam S. Butterworth, Julian P.T. Higgins, Nadeem Sarwar, and John Danesh - Schizophrenia
Lars Bertram
Part IV – Applications of Epidemiologic Methods for Using Genetic Information in Medicine and Public Health
- Mendelian randomization: The contribution to genetic epidemiology to elucidating environmentally modifiable causes of disease
George Davey-Smith and Shah Ebrahim -
Evaluation of predictive genetic tests for common diseases: Bridging epidemiological, clinical, and public health measures
A. Cecile J. W. Janssens, Marta Gwinn, and Muin J. Khoury -
The Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) initiative: Methods of the EGAPP™ working group
Steven M. Teutsch, Linda A. Bradley, Glenn E. Palomaki, James E. Haddow, Margaret Piper, Ned Calonge, W. David Dotson, Michael P. Douglas, and Alfred O. Berg - Rapid evidence-based reviews of genetic tests
James M. Gudgeon, Glenn E. Palomaki, and Marc S. Williams - Role of social and behavioral research in assessing the utility of genetic information
Saskia C. Sanderson , Christopher Wade , and Colleen M. McBride -
Assessing the evidence for clinical utility in newborn screening
Scott D. Grosse - The role of epidemiology in assessing the potential clinical impact of pharmacogenomics
David L. Veenstra - The human epigenome and cancer
Mukesh Verma -
The use of family history in public health practice: the epidemiologic view
Rodolfo Valdez, Muin J. Khoury, and Paula W. Yoon
Part V – Case Studies: Assessing the Use of Genetic Information in Practice for Specific Diseases
- Cytochrome P450 testing in the treatment of depression
Iris Grossman, Mugdha Thakur, and David B. Matchar - A rapid ACCE review of CYP2C9 and VKORC1 allele testing to inform warfarin dosing in adults at elevated risk for thrombotic events to avoid serious bleeding
Monica R. McClain , Glenn E. Palomaki, Margaret Piper, and James E. Haddow - Hereditary hemochromatosis: Population screening for gene mutations
Diana B. Petitti
| Contributors | |
|---|---|
|
Sara R. Bedrosian, BA, BFA McKing Consulting Corporation Office of Public Health Genomics Centers for Disease Control and Prevention Atlanta, GAAlfred O. Berg, MD, MPH Department of Family Medicine University of Washington Seattle, WA Jonine L. Bernstein, PhD Lars Bertram, MD Nick Birkett, MD, MSc Paolo Boffetta, MD Melissa L. Bondy, PhD Linda A. Bradley, PhD Molly S. Bray, PhD Paul E. Brenchley, PhD Philippa Brice, PhD Patricia A. Buffler, PhD, MPH Paul R. Burton, MD Adam S. Butterworth, MSc, PhD Ned Calonge, MD, MPH Harry Campbell, MD, FRCP, FFPH, FRSE Juan Pablo Casas, MD Stephen J. Chanock, MD Anand P. Chokkalingam, PhD, MS Barbara Cohen, PhD John Danesh, MD, MBChB, MSc, DPhil, FRCP George Davey Smith, MD, DSc, FRCP, Alex Demarsh, MSc Siobhan M. Dolan, MD, MPH W. David Dotson, PhD Michael P. Douglas, MS Cornelia M. van Duijn, PhD Ross Duncan, PhD, MA Shah Ebrahim, MSc,DM,FRCP,FFPHM Erik von Elm, MD, MSc Jonine D. Figueroa, PhD Isabel Fortier, PhD Matthew Freedman, MD Helena Furberg, PhD France Gagnon, MSc, PhD Montserrat Garcia-Closas, MD, MPH, DrPH Jean Golding, PhD, DSc, FMedSci Jesus Gonzalez-Bosquet, MD, PhD Jeremy Grimshaw, MBChB, PhD, FRCGP Scott D. Grosse, PhD Iris Grossman, PhD Nelleke A. Gruis, PhD James M. Gudgeon, MS, MBA Marta Gwinn, MD, MPH James E. Haddow, MD Mia Hashibe, PhD Steven Hawken, MSc Julian P.T. Higgins, PhD David J. Hunter, MBBS, ScD Kimberley Hutchings, MSc Claire Infante-Rivard, MD, PhD John P.A. Ioannidis, MD, PhD Cecile J.W. Janssens, PhD Marjo-Riitta Jarvelin, MD, MSc, PhD Candice Y. Johnson, MSc |
Muin J. Khoury, MD, PhD Office of Public Health Genomics Centers for Disease Control and Prevention Atlanta, GA and Division of Cancer Control and Population Sciences National Cancer Institute Bethesda, MDRichard A. King, MD Genetics in Medicine Minneapolis, MN Bartha Knoppers, PhD, O.C. Peter Kraft, PhD Julian Little, PhD Beatrice Malmer, MD, PhD Teri Manolio, MD, PhD Demetrius M. Maraganore, MD Lindsey Masson, PhD, MSc, BSc, RPHNutr David B. Matchar, MD Colleen M. McBride, PhD Mark I. McCarthy, MD, FRCP, FMedSci Monica R. McClain, PhD John McLaughlin, PhD Joyce B.J. van Meurs, PhD David Moher, PhD Julia A. Newton-Bishop, PhD Thomas R. O’Brien, MD, MPH James M. Ostell, PhD Ryan P. Owen, PhD Roberta A. Pagon, MD Glenn E. Palomaki, BS Andrew Paterson, MD Diana B. Petitti, MD, MPH Margaret Piper, PhD Timothy R. Rebbeck, PhD Elio Riboli, PhD Fernando Rivadeneira, MD, PhD Nathaniel Rothman, MD, MPH, MHS Georgia Salanti, PhD Nadeem Sarwar, MPhil, PhD Saskia C. Sanderson, PhD Paul Scheet, PhD Daniela Seminara, PhD, MPH Linda Sharp, PhD Alexandre Stewart, PhD, BScH, MSc Emanuela Taioli, MD, PhD Valerie Tait, PhD Steven M. Teutsch, MD, MPH Mugdha Thakur, MD Evropi Theodoratou, PhD Duncan C. Thomas, PhD Nic Timpson, PhD Andre´ G. Uitterlinden, PhD Rodolfo Valdez, PhD, MSc David L. Veenstra, PhD, PharmD Mukesh Verma, PhD Paolo Vineis, MD, MPH Christopher Wade, PhD, MPH Nick Wareham, PhD, MRC George Wells, MSc, PhD Miriam Wiens, BSc MSc Marc S. Williams, MD Robin E. Williamson, PhD Deborah M. Winn, PhD Paula W. Yoon, ScD, MPH Wei Yu, PhD, MS Maja Zecevic, PhD, MPH Ron Zimmern, MA, FRCP, FFPHM Guang Yong Zou, PhD Eleftheria Zeggini, PhD |
Suggested Citation:
Khoury MJ, Bedrosian S, Gwinn M, Higgins JPT, Ioannidis JPA, Little J, editors. Human Genome Epidemiology (Second Edition): Building the evidence for using genetic information to improve health and prevent disease. New York (NY): Oxford University Press; 2010. Also available with modifications from URL: www.cdc.gov/genomics/resources/books/2009_HuGE/index.htm.
- Page last reviewed: January 6, 2010 (archived document)
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