TABLE III.

Association and prediction for polygenic risk scores based on exon, transcript, and nontranscript SNPs in relation to PanCa using fourfold CV

SNPs in PRS	CV set	Number of SNPs in PRSa	ORb	95% CI	P	R 2c	AUC
Exon SNPsd	1	6,684	1.06	0.96–1.18	0.25	0.011	0.556
	2	6,563	1.11	1.00–1.23	0.05	0.015	0.568
	3	6,626	1.14	1.03–1.27	0.01	0.009	0.551
	4	6,629	1.12	1.01–1.25	0.03	0.012	0.565
Transcript SNPsd	1	13,379	1.10	0.99–1.22	0.09	0.012	0.565
	2	13,183	1.16	1.05–1.29	0.01	0.018	0.576
	3	13,212	1.20	1.08–1.33	0.0008	0.012	0.563
		13,355	1.10	0.99–1.22	0.08	0.011	0.566
Intergenic SNPs	1	10,429	1.05	0.95–1.17	0.33	0.010	0.553
	2	10,520	1.05	0.94–1.16	0.4	0.013	0.562
	3	10,516	1.03	0.93–1.15	0.56	0.005	0.535
	4	10,560	1.10	0.99–1.22	0.08	0.011	0.560

^aSNPs in training set limited to those with low pairwise LD: r² < 0.2 (n = 94,259). The P-value threshold for selecting SNPs from the training set was 0.25.

^bORs based on PRS that has been divided by its standard deviation to generate ORs that correspond to a one standard deviation change in the PRS.

^cGeneralized R² measure for the fitted logistic model.

^dExon and transcript regions were extended on each side by 5 kb and 15 kb, respectively.

PRS, polygenic risk score; CV, cross-validation; OR, odds ratio; CI, confidence interval; AUC, area under the curve.