Significance Test and Genome Selection in Bayesian Shrinkage Analysis

Bayesian shrinkage analysis is the state-of-the-art method for whole genome analysis of quantitative traits. It can estimate the genetic effects for the entire genome using a dense marker map. The technique is now called genome selection. A nice property of the shrinkage analysis is that it can estimate effects of QTL as small as explaining 2% of the phenotypic variance in a typical sample size of 300–500 individuals. In most cases, QTL can be detected with simple visual inspection of the entire genome for the effect because the false positive rate is low. As a Bayesian method, no significance test is needed. However, it is still desirable to put some confidences on the estimated QTL effects. We proposed to use the permutation test to draw empirical thresholds to declare significance of QTL under a predetermined genome wide type I error. With the permutation test, Bayesian shrinkage analysis can be routinely used for QTL detection.