COE: A General Approach for Efficient Genome-Wide Two-Locus Epistasis Test in Disease Association Study

The availability of high density single nucleotide polymorphisms (SNPs) data has made genome-wide association study computationally challenging. Twolocus epistasis (gene-gene interaction) detection has attracted great research interest as a promising method for genetic analysis of complex diseases. In this paper, we propose a general approach, COE, for efficient large scale gene-gene interaction analysis, which supports a wide range of tests. In particular, we show that many commonly used statistics are convex functions. From the observed values of the events in two-locus association test, we can develop an upper bound of the test value. Such an upper bound only depends on single-locus test and the genotype of the SNP-pair. We thus group and index SNP-pairs by their genotypes. This indexing structure can benefit the computation of all convex statistics. Utilizing the upper bound and the indexing structure, we can prune most of the SNP-pairs without compromising the optimality of the re...

• Type: Conference
• Year: 2009
• Where: RECOMB
• Authors: Xiang Zhang, Feng Pan, Yuying Xie, Fei Zou, Wei Wang 0010
• Keywords: Brute Force Approach, Computational Biology, Gene-gene Interaction Analysis, RECOMB 2009, Upper Bound