title: Priors in whole-genome regression: the bayesian alphabet returns.
abstract: Whole-genome enabled prediction of complex traits has received enormous attention in animal and plant breeding and is making inroads into human and even Drosophila genetics. The term "Bayesian alphabet" denotes a growing number of letters of the alphabet used to denote various Bayesian linear regressions that differ in the priors adopted, while sharing the same sampling model. We explore the role of the prior distribution in whole-genome regression models for dissecting complex traits in what is now a standard situation with genomic data where the number of unknown parameters (p) typically exceeds sample size (n). Members of the alphabet aim to confront this overparameterization in various manners, but it is shown here that the prior is always influential, unless n ≫ p. This happens because parameters are not likelihood identified, so Bayesian learning is imperfect. Since inferences are not devoid of the influence of the prior, claims about genetic architecture from these methods should be taken with caution. However, all such procedures may deliver reasonable predictions of complex traits, provided that some parameters ("tuning knobs") are assessed via a properly conducted cross-validation. It is concluded that members of the alphabet have a room in whole-genome prediction of phenotypes, but have somewhat doubtful inferential value, at least when sample size is such that n ≪ p.
authors: Department of Animal Sciences, Department of Biostatistics and Medical Informatics, and Department of Dairy Science, University of Wisconsin, Madison, Wisconsin 53706, USA.
authors: Daniel
authors: D
authors: Gianola
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D001947:Breeding; D015894:Genome, Human; D006801:Humans; D008957:Models, Genetic; D008962:Models, Theoretical; D010641:Phenotype; D010944:Plants / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*; D018401:Sample Size
keywords: Bayesian alphabet; GenPred; SNPs; Shared data resources; genetic architecture; genomic selection; marker-assisted selection; quantitative traits; whole-genome prediction
references: Genet Res (Camb). 2011 Feb;93(1):77-87
references: 21144129
references: Genetics. 2012 Jul;191(3):969-87
references: 22554888
references: J Anim Sci. 2009 Jun;87(6):1883-7
references: 19213705
references: Nat Rev Genet. 2010 Dec;11(12):880-6
references: 21045869
references: BMC Genomics. 2012 Oct 10;13:543
references: 23050763
references: Genetics. 2001 Apr;157(4):1819-29
references: 11290733
references: Genetics. 2009 May;182(1):375-85
references: 19293140
references: BMC Bioinformatics. 2011 May 23;12:186
references: 21605355
references: Genetics. 2012 Dec;192(4):1493-502
references: 23051645
references: PLoS Genet. 2012;8(5):e1002685
references: 22570636
references: PLoS One. 2012;7(11):e49157
references: 23152868
references: PLoS Genet. 2011 Apr;7(4):e1002051
references: 21552331
references: Stat Appl Genet Mol Biol. 2013 Jun;12(3):375-91
references: 23629460
references: PLoS One. 2012;7(7):e40964
references: 22848416
references: Genetics. 2012 Oct;192(2):693-704
references: 22813891
references: Theor Appl Genet. 2012 Aug;125(4):759-71
references: 22566067
references: Genetics. 2009 Sep;183(1):347-63
references: 19620397
references: Genet Res. 2003 Dec;82(3):207-22
references: 15134199
references: Genet Sel Evol. 2009 Jan 05;41:2
references: 19284681
references: J Dairy Sci. 2012 Jul;95(7):4114-29
references: 22720968
references: Genetics. 2010 Nov;186(3):1067-75
references: 20805559
references: Heredity (Edinb). 2013 Mar;110(3):213-9
references: 23149458
references: Genetics. 2012 Dec;192(4):1513-22
references: 23086217
references: Plant Genome. 2010;3(2):106-116
references: 21566722
references: J Dairy Sci. 2009 Oct;92(10):5248-57
references: 19762843
references: J Dairy Sci. 2010 Dec;93(12):5942-9
references: 21094768
references: Genet Res (Camb). 2012 Feb;94(1):21-37
references: 22353246
references: J Dairy Sci. 2012 May;95(5):2723-33
references: 22541502
references: BMC Proc. 2010 Mar 31;4(Suppl 1 Proceedings of the 13th European workshop on QTL map):S5
references: 20380759
references: Genetics. 2013 Feb;193(2):327-45
references: 22745228
references: Curr Genomics. 2012 May;13(3):196-206
references: 23115521
references: J Dairy Sci. 2008 Nov;91(11):4414-23
references: 18946147
references: Genetics. 2006 Aug;173(4):2247-55
references: 16624917
references: Genetics. 2010 Oct;186(2):713-24
references: 20813882