Estimating the posterior probability that genome-wide association findings are true or false.

József BukszárEdwin J C G van den Oord


A limitation of current methods used to declare significance in genome-wide association studies (GWAS) is that they do not provide clear information about the probability that GWAS findings are true of false. This lack of information increases the chance of false discoveries and may result in real effects being missed. We propose a method to estimate the posterior probability that a marker has (no) effect given its test statistic value, also called the local false discovery rate (FDR), in the GWAS. A critical step involves the estimation the parameters of the distribution of the true alternative tests. For this, we derived and implemented the real maximum likelihood function, which turned out to provide us with significantly more accurate estimates than the widely used mixture model likelihood. Actual GWAS data are used to illustrate properties of the posterior probability estimates empirically. In addition to evaluating individual markers, a variety of applications are conceivable. For instance, posterior probability estimates can be used to control the FDR more precisely than Benjamini-Hochberg procedure. The codes are freely downloadable from the web site


Jun 1, 1992·Journal of Personality·T A Widiger, T J Trull
Apr 1, 1980·Journal of Personality and Social Psychology·P T Costa, R R McCrae
Oct 11, 2001·American Journal of Human Genetics·H H GöringJ Blangero
Oct 16, 2001·Nature Genetics·J P IoannidisD G Contopoulos-Ioannidis
Jul 29, 2003·Proceedings of the National Academy of Sciences of the United States of America·John D Storey, Robert Tibshirani
Oct 14, 2004·Bioinformatics·Cyril DalmassoThierry Moreau
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Oct 20, 2006·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Stefanie Scheid, Rainer Spang
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Feb 7, 2008·American Journal of Human Genetics·D Y LinB E Huang
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