ParaHaplo 3.0: A program package for imputation and a haplotype-based whole-genome association study using hybrid parallel computing

We developed a program package for parallel computation of genotype imputation and haplotype reconstruction. Our program package, ParaHaplo 3.0, is intended for use in workstation clusters using the Intel Message Passing Interface. We compared the performance of ParaHaplo 3.0 on the Japanese in Tokyo, Japan and Han Chinese in Beijing, and Chinese in the HapMap dataset. A parallel version of ParaHaplo 3.0 can conduct genotype imputation 20 times faster than a non-parallel version of ParaHaplo.ParaHaplo 3.0 is an invaluable tool for conducting haplotype-based GWASs. The need for faster genotype imputation and haplotype reconstruction using parallel computing will become increasingly important as the data sizes of such projects continue to increase. ParaHaplo executable binaries and program sources are available at http://en.sourceforge.jp/projects/parallelgwas/releases/ webcite.Recent advances in various high-throughput genotyping technologies have allowed us to test allelic frequency differences between case and control populations on a genome-wide scale [1]. Genome-wide association studies (GWASs) are used to compare the frequency of alleles or genotypes of a particular variant between cases and controls for a particular disease across a given genome [2-4]. More than a million single nucleotide polymorphisms (SNPs) are analyzed in SNP-based GWASs and haplotype-based GWASs [5,6].By modeling the patterns of linkage disequilibrium in a reference panel, genotypes not directly measured in the study samples can be imputed [7]. SNP genotype imputation has been proposed as a powerful means to include genetic markers into large-scale disease association studies without the need to actually genotype them [8,9]To quickly conduct GWASs, we developed a software package for the parallel computation of genotype imputation and haplotype reconstruction called ParaHaplo 3.0. ParaHaplo 3.0 contains all of the functions of ParaHaplo 1.0 [5] and ParaHaplo 2.0 [6], plus it can conduct ge