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

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

Univariate Bivariate Filter Bivariate Filter + GSS
Dataset log10 P χ 2   χ 2   DSS GBOOST   χ 2 DSS GBOOST
HT -9.8   128   429 51   41 107 24
BD -10.9   2445   556 34   44 179 27
CAD -13.1   210147   7807 43   42 116 39
T2D -13.3   56592   3105 52   79 134 41
CD -34.3   > 500000   5591 25   29 57 22
RA -37.7   > 500000   823 99   59 312 95
T1D -133.6   > 500000   4993 37   2 107 33
  1. 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.