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

Table 1 Estimated best combinations of two SNPs on the occurrence of breast cancer

Combined SNP number (specific SNPs)		SNP Genotypes	Control number / Case number	CC	SN	SP	Average	Odds Ratio (95%CI)	p-value
High-risk	Two SNPs	Other	330/209
	SNPs (4, 7)	2-3	4/11	0.616	0.050	0.988	0.551	4.342 (1.259-16.394)	0.013
	SNPs (4, 7)	2-3	(Diff. = 7)	0.616	0.050	0.988	0.551	4.342 (1.259-16.394)	0.013
	Two SNPs	Other	327/209
	SNPs (4, 6)	3-2	7/11	0.610	0.050	0.979	0.546	2.459 (0.867-7.143)	0.084
	SNPs (4, 6)	3-2	(Diff. = 4)	0.610	0.050	0.979	0.546	2.459 (0.867-7.143)	0.084
	Two SNPs	Other	289/172
	SNPs (3, 5)	2-1	45/48	0.608	0.218	0.865	0.564	1.792 (1.118-2.875)	0.014
	SNPs (3, 5)	2-1	(Diff. = 3)	0.608	0.218	0.865	0.564	1.792 (1.118-2.875)	0.014
Low-risk	Two SNPs	Other	197/151
	SNPs (3, 4)	1-1	137/69	0.480	0.314	0.589	0.461	0.657 (0.452-0.955)	0.025
	SNPs (3, 4)	1-1	(Diff. = 68)	0.480	0.314	0.589	0.461	0.657 (0.452-0.955)	0.025
	Two SNPs	Other	226/174
	SNPs (3, 7)	1-2	108/46	0.491	0.209	0.676	0.459	0.553 (0.364-0.839)	0.004
	SNPs (3, 7)	1-2	(Diff. = 62)	0.491	0.209	0.676	0.459	0.553 (0.364-0.839)	0.004
	Two SNPs	Other	223/168
	SNPs (1, 3)	2-1	111/52	0.496	0.236	0.668	0.467	0.622 (0.415-0.931)	0.017
	SNPs (1, 3)	2-1	(Diff. = 59)	0.496	0.236	0.668	0.467	0.622 (0.415-0.931)	0.017

^{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.