Table 6.

R² and p-values from likelihood ratio test for polygenic prediction using BLUP, GRS and PCs in 10-fold cross-validation

(a) BLUP included all SNPs available from genome-wide SNP chip after LD-pruning
		Hair color		Tanning ability		Basal cell carcinomaa
Model		R2	P-valueb	R2	P-valueb	R2	P-valueb
1	BLUPunadj	0.0588	<10−16	0.0131	<10−16	0.0125	2.93 × 10−13
2	BLUPadj	0.0045	5.86 × 10−9	0.0001	0.385	0.0013	0.0112
3	BLUPadj + PC1 + … + PC5	0.0781	<10−16	0.0345	<10−16	0.0218	<10−16

(b) GRS including genome-wide significant SNPs; BLUP excluded SNPs in LD with genome-wide significant SNPs but all other SNPs
		Hair color		Tanning ability		Basal cell carcinomaa
Model		R2	P-valueb	R2	P-valueb	R2	P-valueb
4	BLUPunadj,-gs + GRSunadj	0.2350	<10−16	0.1221	8.07 × 10−1	0.0275	6.49 × 10−7
5	BLUPadj,-gs + GRSadj	0.2258	8.10 × 10−3	0.1233	2.97 × 10−6	0.0208	5.52 × 10−2
6	BLUPadj,-gs + GRSadj + PC1 + … + PC5	0.2413	<10−16	0.1308	<10−16	0.0359	3.83 × 10−15

^aR² on liability scale

^bP-values are from likelihood ratio tests comparing model 1 and 2 to the null model, model 3 to model 2, model 4 and 5 to the corresponding models with only GRS, and model 6 to model 5.

_-gs denotes excluding genome-wide significant SNPs.