ParaHaplo: A program package for haplotype-based whole-genome association study using parallel computing

Since more than one million of single nucleotide polymorphisms (SNPs) are analyzed in genome-wide association study (GWAS), multiple comparisons are problematic. To cope with multiple-comparison problems in GWAS, haplotype-based algorithms were developed to correct for the multiple comparisons at multiple SNP loci in linkage disequilibrium.

The permutation test can also control problems inherent in multiple testing; however, the calculation of exact probability and the execution of permutation tests are both time-consuming. aster methods for calculating exact probabilities and executing permutation tests are required.

Methods: We developed a set of computer programs for the parallel computation of accurate P values in haplotype-based GWAS.

Our program, ParaHaplo, is targeted to workstation clusters using the Intel Message Passing Interface (MPI). We compared the performance of our algorithm with that of the regular permutation test on CHB and JPT of HapMap.

Results: ParaHaplo can detect smaller difference between two populations than SNP-based GWAS.

We also found that parallel-computing technique made ParaHaplo 100-fold faster than non-parallel version of the program.

Conclusion: ParaHaplo is a useful tool for haplotype-based GWAS. The executable binaries and program sources of ParaHaplo are available at http://sourceforge.jp/projects/parallelgwas/?_sl=1.

Author: Kazuharu MisawaNaoyuki Kamatani
Credits/Source: Source Code for Biology and Medicine 2009, 4:7

Published on: 2009-10-21

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