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Table 6 Total Chi8 and GBOOST time in hours to run on the seven WTCCC GWAS dataset

From: Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test

Data T1D RA CD CAD T2D HT BD
Time
 Chi8 14.2 10.1 8.4 8.6 8.6 8.7 8.3
 GBOOST 1.7 1.6 1.6 1.6 1.6 1.6 1.5
Number of significant pairs
 Chi8 1644 11 4 0 0 0 0
 GBOOST 28K 11K 9.9K 10K 10K 10K 9.8K
 GBOOST* 92 0 0 0 0 0 0
 BOOST (published [14]) 91 0 1 0 0 0 0
Number of common pairs between Chi8 and GBOOST
  236 2 4 NA NA NA NA
  1. We also show number of significant pairs outputted by each program such that both SNPs are insignificant on their own. Otherwise our program Chi8 outputs thousands of interactions where one SNP is significant on its own. For GBOOST we use the same interaction threshold of 37 as we did for the simulated data. We also constrain the GBOOST output (denoted as GBOOST*) to consider just pairs with a threshold above 175 and at least 100 SNPs apart to account for linkage. We selected this threshold so as to output a similar number of pairs for type 1 diabetes as published in the original BOOST paper [14]. The previously published values from the original BOOST study consider pairs that are at least 1MB apart and individually insignificant [14]