TY - JOUR
T1 - DAIRRy-BLUP: A High-Performance Computing Approach to Genomic Prediction
JF - Genetics
JO - Genetics
SP - 813
LP - 822
M3 - 10.1534/genetics.114.163683
VL - 197
IS - 3
AU - Coninck, Arne De
AU - Fostier, Jan
AU - Maenhout, Steven
AU - De Baets, Bernard
Y1 - 2014/07/01
UR - http://www.genetics.org/content/197/3/813.abstract
N2 - In genomic prediction, common analysis methods rely on a linear mixed-model framework to estimate SNP marker effects and breeding values of animals or plants. Ridge regressionâ€“best linear unbiased prediction (RR-BLUP) is based on the assumptions that SNP marker effects are normally distributed, are uncorrelated, and have equal variances. We propose DAIRRy-BLUP, a parallel, Distributed-memory RR-BLUP implementation, based on single-trait observations (y), that uses the Average Information algorithm for restricted maximum-likelihood estimation of the variance components. The goal of DAIRRy-BLUP is to enable the analysis of large-scale data sets to provide more accurate estimates of marker effects and breeding values. A distributed-memory framework is required since the dimensionality of the problem, determined by the number of SNP markers, can become too large to be analyzed by a single computing node. Initial results show that DAIRRy-BLUP enables the analysis of very large-scale data sets (up to 1,000,000 individuals and 360,000 SNPs) and indicate that increasing the number of phenotypic and genotypic records has a more significant effect on the prediction accuracy than increasing the density of SNP arrays.
ER -