Significance test and genome selection in bayesian shrinkage analysis.

International Journal of Plant Genomics
Xiaohong Che, Shizhong Xu

Abstract

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.

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Citations

Oct 2, 2012·Briefings in Bioinformatics·Yongxin LiuRunqing Yang
Jun 18, 2014·Human Genetics·Evangelina López de MaturanaNúria Malats
Mar 8, 2012·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·S M NalailaZ Wang
Apr 10, 2015·PloS One·Leena PasanenMikko J Sillanpää
Mar 25, 2011·Genetics Research·Shizhong Xu, Zhiqiu Hu
Sep 18, 2012·Genetics·Crispin M Mutshinda, Mikko J Sillanpää
Sep 2, 2010·Genetics·Xin ChenShizhong Xu
Aug 8, 2012·G3 : Genes - Genomes - Genetics·Fuping Zhao, Shizhong Xu

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Software Mentioned

pLOD
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