Bayes Factors for Genome-Wide Association Studies: Comparison with P-values

被引:268
作者
Wakefield, Jon [1 ]
机构
[1] Univ Washington, Dept Biostat, Seattle, WA 98195 USA
基金
美国国家卫生研究院;
关键词
Bonferroni correction; P-values; prior distributions; strength of evidence; PROBABILITY; PARAMETERS; IMPUTATION; FALSE;
D O I
10.1002/gepi.20359
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
The Bayes factor is a summary measure that provides an alternative to the P-value for the ranking of associations, or the flagging of associations as -significant". We describe an approximate Bayes factor that is straightforward to use and is appropriate when sample sizes are large. We consider various choices of the prior oil the effect size, including those that allow effect size to vary with the minor allele frequency (MAF) of the marker. All important contribution is the description of a specific prior Thai gives identical rankings between Bayes factors and P-values, providing a link between the two approaches, and allowing the implications of the use of P-values to be more easily understood. As a summary measure of noteworthiness P-values are difficult to calibrate since their interpretation depends oil MAF and, crucially, oil sample size. A consequence is that a consistent decision-making procedure using P-values requires a threshold for significance that reduces with sample size, contrary to common practice. Genet. Epidemiol. 33:79-86, 2009. (C) 2008 Wiley-Liss, Inc.
引用
收藏
页码:79 / 86
页数:8
相关论文
共 32 条
[1]   THE LARGE-SAMPLE CORRESPONDENCE BETWEEN CLASSICAL HYPOTHESIS TESTS AND BAYESIAN POSTERIOR ODDS TESTS [J].
ANDREWS, DWK .
ECONOMETRICA, 1994, 62 (05) :1207-1232
[2]   A tutorial on statistical methods for population association studies [J].
Balding, David J. .
NATURE REVIEWS GENETICS, 2006, 7 (10) :781-791
[3]   Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls [J].
Burton, Paul R. ;
Clayton, David G. ;
Cardon, Lon R. ;
Craddock, Nick ;
Deloukas, Panos ;
Duncanson, Audrey ;
Kwiatkowski, Dominic P. ;
McCarthy, Mark I. ;
Ouwehand, Willem H. ;
Samani, Nilesh J. ;
Todd, John A. ;
Donnelly, Peter ;
Barrett, Jeffrey C. ;
Davison, Dan ;
Easton, Doug ;
Evans, David ;
Leung, Hin-Tak ;
Marchini, Jonathan L. ;
Morris, Andrew P. ;
Spencer, Chris C. A. ;
Tobin, Martin D. ;
Attwood, Antony P. ;
Boorman, James P. ;
Cant, Barbara ;
Everson, Ursula ;
Hussey, Judith M. ;
Jolley, Jennifer D. ;
Knight, Alexandra S. ;
Koch, Kerstin ;
Meech, Elizabeth ;
Nutland, Sarah ;
Prowse, Christopher V. ;
Stevens, Helen E. ;
Taylor, Niall C. ;
Walters, Graham R. ;
Walker, Neil M. ;
Watkins, Nicholas A. ;
Winzer, Thilo ;
Jones, Richard W. ;
McArdle, Wendy L. ;
Ring, Susan M. ;
Strachan, David P. ;
Pembrey, Marcus ;
Breen, Gerome ;
St Clair, David ;
Caesar, Sian ;
Gordon-Smith, Katherine ;
Jones, Lisa ;
Fraser, Christine ;
Green, Elain K. .
NATURE, 2007, 447 (7145) :661-678
[4]   Maximum likelihood inference on a mixed conditionally and marginally specified regression model for genetic epidemiologic studies with two-phase sampling [J].
Chatterjee, Nilanjan ;
Chen, Yi-Hau .
JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 2007, 69 :123-142
[5]   Problems of reporting genetic associations with complex outcomes [J].
Colhoun, HM ;
McKeigue, PM ;
Smith, GD .
LANCET, 2003, 361 (9360) :865-872
[6]  
Cox DR., 1974, THEORETICAL STAT
[7]   Parameters for reliable results in genetic association studies in common disease [J].
Dahlman, I ;
Eaves, IA ;
Kosoy, R ;
Morrison, VA ;
Heward, J ;
Gough, SCL ;
Allahabadia, A ;
Franklyn, JA ;
Tuomilehto, J ;
Tuomilehto-Wolf, E ;
Cucca, F ;
Guja, C ;
Ionescu-Tirgoviste, C ;
Stevens, H ;
Carr, P ;
Nutland, S ;
McKinney, P ;
Shield, JP ;
Wang, W ;
Cordell, HJ ;
Walker, N ;
Todd, JA ;
Concannon, P .
NATURE GENETICS, 2002, 30 (02) :149-150
[8]   HTRA1 promoter polymorphism in wet age-related macular degeneration [J].
DeWan, Andrew ;
Liu, Mugen ;
Hartman, Stephen ;
Zhang, Samuel Shao-Min ;
Liu, David T. L. ;
Zhao, Connie ;
Tam, Pancy O. S. ;
Chan, Wai Man ;
Lam, Dennis S. C. ;
Snyder, Michael ;
Barnstable, Colin ;
Pang, Chi Pui ;
Hoh, Josephine .
SCIENCE, 2006, 314 (5801) :989-992
[9]   Genome-wide association study identifies novel breast cancer susceptibility loci [J].
Easton, Douglas F. ;
Pooley, Karen A. ;
Dunning, Alison M. ;
Pharoah, Paul D. P. ;
Thompson, Deborah ;
Ballinger, Dennis G. ;
Struewing, Jeffery P. ;
Morrison, Jonathan ;
Field, Helen ;
Luben, Robert ;
Wareham, Nicholas ;
Ahmed, Shahana ;
Healey, Catherine S. ;
Bowman, Richard ;
Meyer, Kerstin B. ;
Haiman, Christopher A. ;
Kolonel, Laurence K. ;
Henderson, Brian E. ;
Le Marchand, Loic ;
Brennan, Paul ;
Sangrajrang, Suleeporn ;
Gaborieau, Valerie ;
Odefrey, Fabrice ;
Shen, Chen-Yang ;
Wu, Pei-Ei ;
Wang, Hui-Chun ;
Eccles, Diana ;
Evans, D. Gareth ;
Peto, Julian ;
Fletcher, Olivia ;
Johnson, Nichola ;
Seal, Sheila ;
Stratton, Michael R. ;
Rahman, Nazneen ;
Chenevix-Trench, Georgia ;
Bojesen, Stig E. ;
Nordestgaard, Borge G. ;
Axelsson, Christen K. ;
Garcia-Closas, Montserrat ;
Brinton, Louise ;
Chanock, Stephen ;
Lissowska, Jolanta ;
Peplonska, Beata ;
Nevanlinna, Heli ;
Fagerholm, Rainer ;
Eerola, Hannaleena ;
Kang, Daehee ;
Yoo, Keun-Young ;
Noh, Dong-Young ;
Ahn, Sei-Hyun .
NATURE, 2007, 447 (7148) :1087-U7
[10]  
EFRON B, 2001, I MATH STAT LECT NOT, P208