GWIS - model-free, fast and exhaustive search for epistatic interactions in case-control GWAS

BMC Genomics

Table 3 Summary of the number of SNP pairs detected by different filtering methods.

Summary of the number of SNP pairs detected by $χ^{2}$ , GBOOST and our introduced DSS heuristic over all WTCCC datasets before and after filtering with GSS. The rows of the table are sorted in descending order of p-values for univariate $χ^{2}$ test (Column 2). Columns 3-5 show results for the bivariate filters, and columns 6-8 show the number of epistatic interactions discovered after further filtering with GSS. In some diseases, strong univariate SNPs likely cause proliferation of non-epistatic but significant pairs according to $χ^{2}$ . These pairs are largely removed by the proposed GSS filter. A '*' indicates that an upper bound on the number of recorded pairs was reached. The number of significant pairs may be much higher.

ISSN: 1471-2164