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


RESULTS
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.


BACKGROUND
The codes are freely downloadable from the web site http://www.people.vcu.edu/~jbukszar.
Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Medical College of Virginia, Virginia Commonwealth University, 1112 East Clay Street, PO Box 980533, Richmond, Virginia 23298, USA. jbukszar@vcu.edu
József
J
Bukszár
Joseph L
JL
McClay
Edwin J C G
EJ
van den Oord
D017360:Arabidopsis / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods; D055106:Genome-Wide Association Study / Q000379:methods*; D011336:Probability