Table 4.

Pathway analysis results for lethal prostate cancer and gene sets in the vitamin D pathway

Gene	Chromosome	Size, kb	No. of SNPs included*	Global P from kernel machine analysis†	Global P from kernel machine analysis adjusted for 25(OH)D†
VDR	12	63.49	28	.01	.01
CYP27B1	12	4.86	3	.75	.70
GC	4	42.48	12	.80	.65
CYP27A1	20	20.54	5	.02	.02
CYP2R1	2	33.31	6	.14	.10
CYP24A1	11	14.2	18	.45	.45
RXRA	9	114	20	.09	.10
Total Pathway			92	.008	.006

^*Ninety-seven SNPs originally selected; two SNPs failed genotyping; two were out of Hardy–Weinberg equilibrium, at P < .001; and one was eliminated because frequency in sample did not match that of phased haplotypes for imputation; therefore, a total of 92 SNPs were included in pathway analysis.

^†P values were calculated using a logistic kernel machine model and were two-sided.