Table 3.

Top Results from the Logistic Kernel-Machine-Based SNP-Set Analysis of the CGEMS Breast Cancer Study Data

	Linear		IBS		Weighted IBS
Gene	p Value	q-Value	p Value	q-Value	p Value	q-Value
FGFR2	7.69 × 10−7	0.01	2.53 × 10−6	0.03	1.35 × 10−5	0.05
CNGA3	5.59 × 10−6	0.05	4.65 × 10−6	0.03	3.25 × 10−6	0.02
TBK1	1.30 × 10−5	0.07	3.28 × 10−6	0.03	5.48 × 10−6	0.02
VWA3B	1.53 × 10−5	0.07	7.84 × 10−6	0.03	3.99 × 10−6	0.02
PTCD3	5.50 × 10−5	0.20	9.02 × 10−6	0.03	3.78 × 10−6	0.02
XPOT	6.60 × 10−5	0.20	3.48 × 10−5	0.09	4.91 × 10−5	0.11
VAPB	9.79 × 10−5	0.22	4.51 × 10−5	0.10	8.11 × 10−5	0.14
SHC3	1.01 × 10−4	0.22	3.77 × 10−4	0.34	1.61 × 10−3	0.46
SFTPB	1.78 × 10−4	0.31	1.38 × 10−4	0.27	7.62 × 10−5	0.14
SPATA7	1.90 × 10−4	0.31	1.76 × 10−4	0.28	1.39 × 10−4	0.22