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

BMC Genomics

Table 4 Overlap between SNP pairs found by GWIS using the DSS filter and previous studies after GSS filtering.

Disease	Lit. total	Lit. after GSS	Overlap	GWIS only	GWIS total
BD	134	57 (43%)	56	123 (69%)	179
CAD	117	37 (32%)	37	79 (68%)	116
CD	234	21 (9%)	21	36 (63%)	57
HT	93	53 (57%)	49	58 (54%)	107
RA	293	191 (65%)	190	122 (39%)	312
T1D	801	35 (4%)	35	72 (67%)	107
T2D	230	59 (26%)	56	78 (58%)	134

Overlap between SNP pairs found by GWIS and previous studies. "Lit. total" refers to the number of SNP pairs previously reported. "Lit. after GSS" refers to the number of pairs that remain significant after applying the GSS filter. "Overlap" is the set of pairs detected by GWIS and reported in literature. GWIS only and GWIS total refer to the number of pairs only detected by GWIS and the total number of pairs detected by GWIS respectively. Significance for DSS and GSS is defined by Bonferroni correction $(p - value = {(\begin{matrix} 459, 012 \\ 2 \end{matrix})}^{- 1} \approx 1 0^{- 11})$ .

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