Extended Bayesian LASSO for multiple quantitative trait loci mapping and unobserved phenotype prediction.
The Bayesian LASSO (BL) has been pointed out to be an effective approach to sparse model representation and successfully applied to quantitative trait loci (QTL) mapping and genomic breeding value (GBV) estimation using genome-wide dense sets of markers. However, the BL relies on a single parameter known as the regularization parameter to simultaneously control the overall model sparsity and the shrinkage of individual covariate effects. This may be idealistic when dealing with a large number of predictors whose effect sizes may differ by orders of magnitude. Here we propose the extended Bayesian LASSO (EBL) for QTL mapping and unobserved phenotype prediction, which introduces an additional level to the hierarchical specification of the BL to explicitly separate out these two model features. Compared to the adaptiveness of the BL, the EBL is "doubly adaptive" and thus, more robust to tuning. In simulations, the EBL outperformed the BL in regard to the accuracy of both effect size estimates and phenotypic value predictions, with comparable computational time. Moreover, the EBL proved to be less sensitive to tuning than the related Bayesian adaptive LASSO (BAL), which introduces locus-specific regularization parameters as well, but involves no mechanism for distinguishing between model sparsity and parameter shrinkage. Consequently, the EBL seems to point to a new direction for QTL mapping, phenotype prediction, and GBV estimation.
Mutshinda
Crispin M
CM
Department of Agricultural Sciences, University of Helsinki, Helsinki FIN-00014, Finland.
Sillanpää
Mikko J
MJ
D001499:Bayes Theorem; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D030541:Databases, Genetic; D005819:Genetic Markers; D001467:Hordeum / Q000235:genetics; D008957:Models, Genetic; D010641:Phenotype; D040641:Quantitative Trait Loci / Q000235:genetics*; D015203:Reproducibility of Results
D005819:Genetic Markers
PLoS Genet. 2007 Jul;3(7):e114
17676998
Genet Res (Camb). 2009 Dec;91(6):427-36
20122298
Genetics. 2001 Sep;159(1):371-87
11560912
Genet Res. 2000 Apr;75(2):249-52
10816982
PLoS Genet. 2008 Oct;4(10):e1000231
18949033
Genetics. 2010 May;185(1):349-59
20157003
Heredity (Edinb). 2005 Jul;95(1):96-104
15931238
Genetics. 2009 May;182(1):375-85
19293140
Genetics. 2005 May;170(1):465-80
15781696
Genetics. 2007 Apr;175(4):1955-63
17277367
Bioinformatics. 2009 Mar 15;25(6):714-21
19176549
Genetics. 2003 Feb;163(2):789-801
12618414
Genet Res (Camb). 2009 Feb;91(1):23-37
19220929
Am J Hum Genet. 2008 Feb;82(2):375-85
18252218
Heredity (Edinb). 2009 Sep;103(3):223-37
19455182
Genetics. 2008 Jun;179(2):1045-55
18505874
Biometrics. 2007 Jun;63(2):513-21
17688503
Heredity (Edinb). 2008 Sep;101(3):271-84
18648392
Genetics. 1994 Nov;138(3):963-71
7851788