Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide ass

Background: Genome-wide association studies (GWAS) using single nucleotide polymorphism (SNP) markers provide opportunities to detect epistatic SNPs associated with quantitative traits and to detect the exact mode of an epistasis effect. Computational difficulty is the main bottleneck for epistasis testing in large scale GWAS. Results: The EPISNPmpi and EPISNP computer programs were developed for testing single-locus and epistatic SNP effects on quantitative traits in GWAS, including tests of three single-locus effects for each SNP (SNP genotypic effect, additive and dominance effects) and five epistasis effects for each pair of SNPs (two-locus interaction, additive

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Li Ma, H. Birali Runesha, Daniel Dvorkin, John R. Garbe, Yang Da
• Keywords: BMCBI 2008, Computing Programs, Epistasis Testing, Large Scale