Genomic selection and complex trait prediction using a fast EM algorithm applied to genome-wide markers

BMC Bioinformatics

Research Article

John A Woolliams¹  Theo HE Meuwissen²  Ross K Shepherd³ 

[1] Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9PS, Roslin, Midlothian, UK;Institute Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Box 5003, N1432 As, Norway;School of Information and Communication Technology, CQUniversity, 4702, Rockhampton, Australia;

关键词: Quantitative Trait Locus;    Single Nucleotide Polymorphism;    Lasso;    Genomic Selection;    Expectation Maximization Algorithm;   

DOI  :  10.1186/1471-2105-11-529

 received in 2010-06-04, accepted in 2010-10-22,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundThe information provided by dense genome-wide markers using high throughput technology is of considerable potential in human disease studies and livestock breeding programs. Genome-wide association studies relate individual single nucleotide polymorphisms (SNP) from dense SNP panels to individual measurements of complex traits, with the underlying assumption being that any association is caused by linkage disequilibrium (LD) between SNP and quantitative trait loci (QTL) affecting the trait. Often SNP are in genomic regions of no trait variation. Whole genome Bayesian models are an effective way of incorporating this and other important prior information into modelling. However a full Bayesian analysis is often not feasible due to the large computational time involved.ResultsThis article proposes an expectation-maximization (EM) algorithm called emBayesB which allows only a proportion of SNP to be in LD with QTL and incorporates prior information about the distribution of SNP effects. The posterior probability of being in LD with at least one QTL is calculated for each SNP along with estimates of the hyperparameters for the mixture prior. A simulated example of genomic selection from an international workshop is used to demonstrate the features of the EM algorithm. The accuracy of prediction is comparable to a full Bayesian analysis but the EM algorithm is considerably faster. The EM algorithm was accurate in locating QTL which explained more than 1% of the total genetic variation. A computational algorithm for very large SNP panels is described.ConclusionsemBayesB is a fast and accurate EM algorithm for implementing genomic selection and predicting complex traits by mapping QTL in genome-wide dense SNP marker data. Its accuracy is similar to Bayesian methods but it takes only a fraction of the time.

【 授权许可】

CC BY   
© Shepherd et al; licensee BioMed Central Ltd. 2010