SNP-SNP interactions in breast cancer susceptibility

BMC Cancer

Table 4 Analysis of two-way SNP interaction effects on breast cancer.

Two-way Interactions between polymorphisms	Crude P-values ^‡	Bootstrap frequency of stepwise variable selection*	Bootstrap P-values ^†	FDR adjusted P-values ^§	FPRP ^¶
XPD-[Lys751Gln] and IL10-[G(-1082)A]	0.035	68%	0.001	*0.007*	*0.092*
COMT-[Met108/158Val] and CCND1-[Pro241Pro]	0.010	61%	0.002	*0.014*	*0.169*
GSTP1-[Ile105Val] and COMT-[Met108/158Val]	0.036	54%	0.001	*0.007*	*0.093*
CYP17-[C(518)T] and GADD45-[C(IVS3+168)T]	0.024	53%	0.018	0.062	0.999
BARD1-[Pro24Ser] and ESR1-[Pro325Pro]	0.039	51%	ns ^\|\|	ns	-
TNFA-[G(-308)A] and p27-[Val109Gly]	0.016	49%	0.025	*0.079*	0.996
BARD1-[Pro24Ser] and p27-[Val109Gly]	0.021	44%	ns	ns	-
BARD1-[Pro24Ser] and XPD-[Lys751Gln]	0.024	36%	0.002	*0.014*	0.671
ESR1-[Ser10Ser] and ESR1-[Pro325Pro]	0.028	30%	0.097	ns	0.999

^‡ Probability to enter the model in the stepwise multivariable model based on the score statistic in the original data set.
*Proportion of times the interaction is selected by the stepwise multivariable model in the 1,000 bootstrap samples.
^† P-values estimated by bootstrap analysis in the 1,000 random samples.
^§False Discovery Rate (FDR) adjusted P-values.
^||ns: p > 0.10.
^¶False Positive Report Probability

ISSN: 1471-2407