LAMPLINK: detection of statistically significant SNP combinations from GWAS data

Summary: One of the major issues in genome-wide association studies is to solve the missing heritability problem. While considering epistatic interactions among multiple SNPs may contribute to solving this problem, existing software cannot detect statistically significant high-order interactions. We propose software named LAMPLINK, which employs a cutting-edge method to enumerate statistically significant SNP combinations from genome-wide case–control data. LAMPLINK is implemented as a set of additional functions to PLINK, and hence existing procedures with PLINK can be applicable. Applied to the 1000 Genomes Project data, LAMPLINK detected a combination of five SNPs that are statistically significantly accumulated in the Japanese population. Availability and Implementation: LAMPLINK is available at http://a-terada.github.io/lamplink/. Contact: terada@cbms.k.u-tokyo.ac.jp or sese.jun@aist.go.jp Supplementary information: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics - Category: Bioinformatics Authors: Tags: GENETICS AND POPULATION ANALYSIS Source Type: research