Improved branch and bound algorithm for detecting SNP-SNP interactions in breast cancer

Table 3 Estimated best combinations of SNPs on the occurrence of breast cancer in the low risk group

Combined SNP number (specific SNPs)	SNP Genotypes	Control number / Case number	CC	SN	SP	Average	Odds Ratio (CI)	p-value
Two SNPs	Other	197/151
SNPs (3, 4)	1-1	137/69	0.480	0.314	0.600	0.465	0.657 (0.452-0.955)	0.025
		(Diff. = 68)
Three SNPs	Other	260/189
SNPs (1, 3, 5)	2-1-1	74/31	0.525	0.141	0.778	0.481	0.576 (0.355-0.934)	0.020
SNPs (1, 3, 5)	2-1-1	(Diff. = 43)	0.525	0.141	0.778	0.481	0.576 (0.355-0.934)	0.020
Four SNPs	Other	294/207
SNPs (1, 2, 3, 4)	2-2-1-1	40/13	0.554	0.059	0.880	0.498	0.462 (0.228-0.919)	0.018
SNPs (1, 2, 3, 4)	2-2-1-1	(Diff. = 27)	0.554	0.059	0.880	0.498	0.462 (0.228-0.919)	0.018
Five SNPs	Other	310/215
SNPs (1, 2, 3, 4, 5)	2-2-1-1-1	24/5	0.569	0.023	0.928	0.507	0.300 (0.099-0.846)	0.011
SNPs (1, 2, 3, 4, 5)	2-2-1-1-1	(Diff. = 19)	0.569	0.023	0.928	0.507	0.300 (0.099-0.846)	0.011
Six SNPs	Other	323/218
SNPs (1, 2, 3, 4, 5, 6)	2-2-1-1-1-2	11/2	0.587	0.009	0.967	0.521	0.269 (0.041-1.301)	0.070
SNPs (1, 2, 3, 4, 5, 6)	2-2-1-1-1-2	(Diff. = 9)	0.587	0.009	0.967	0.521	0.269 (0.041-1.301)	0.070
Seven SNPs	Other	325/219
SNPs (1, 2, 3, 4, 5, 6, 7)	2-2-1-1-1-2-1	9/1	0.588	0.005	0.973	0.522	0.165 (0.008-1.277)	0.098
SNPs (1, 2, 3, 4, 5, 6, 7)	2-2-1-1-1-2-1	(Diff. = 8)	0.588	0.005	0.973	0.522	0.165 (0.008-1.277)	0.098

^{NOTE -} Other: The reference group, indicating the union of all other possible two to seven SNP combinations; N.E: Not estimable; CC: Correct; SN: Sensitivity; SP: Specificity.