Genome-wide analysis of haplotype interaction for the data from the North American Rheumatoid Arthritis Consortium

Recent genome-wide association studies on several complex diseases have focused on individual single-nucleotide polymorphism (SNP) analysis; however, not many studies have reported interactions among genes perhaps because the gene-gene and gene-environment interaction analysis could be infeasible due to heavy computing requirements. In this study we propose a new strategy for exploring the interactions among haplotypes. The proposed method consists of two steps. Step 1 tests the single-SNP association of whole genome with multiple testing corrections and finds the haplotype blocks of the significant SNPs. Step 2 performs interaction analysis of haplotypes within blocks. Our proposed method is applied to the rheumatoid arthritis data for Genetic Analysis Workshop 16.