Table 3.

Meta-analysis of percentage of variance explained in depression phenotype in NHS by the genome-wide agnostic polygenic scores in the leave-one-substudy-out analysis (N = 6989).

Cumulative P-value thresholds for selecting SNPs			Nonoverlapping P-value thresholds for selecting SNPs
Ptraining1 threshold	Percentage of variance explained	P-value	Ptraining1 threshold	Percentage of variance explained	P-value
p<0.00001	0.1	0.355	0–0.00001	0.1	0.355
p<0.0001	0	0.528	0.00001–0.0001	0	0.944
p<0.001	0.2	0.159	0.0001–0.001	0.2	0.118
p<0.01	0.1	0.524	0.001–0.01	0.1	0.977
p<0.1	0.1	0.043	0.01–0.1	0.1	0.013
p<0.2	0.1	0.002	0.1–0.2	0.1	0.003
p<0.3	0.2	0.003	0.2–0.3	0.1	0.832
p<0.4	0.1	0.002	0.3–0.4	0.1	0.269
p<0.5	0.1	0.004	0.4–0.5	0	0.996

NHS, Nurses' Health Study; SNP, single-nucleotide polymorphism.

¹Training set: remaining three NHS substudies except the testing sample.