Table 3.

The predicted AUC values for C+T, LDpred, and LDpred2 with different parameters in the simulation experiment based on the UKBB data

C+T
Threshold	1	5e − 1	5e − 2	5e − 3	5e − 4	5e − 5	5e − 6	5e − 7	5e − 8
PRStuning	0.789	0.790	0.816	0.830	0.834	0.835	0.835	0.835	0.835
Testing	0.793	0.795	0.830	0.852	0.860	0.865	0.867	0.868	0.868
LDpred
π	1	3e − 1	1e − 1	3e − 2	1e − 2	3e − 3	1e − 3	3e − 4	1e − 4	3e − 5	1e − 5
PRStuning	0.747	0.784	0.732	0.593	0.550	0.532	0.519	0.513	0.509	0.504	0.502
Testing	0.790	0.813	0.749	0.588	0.548	0.527	0.518	0.509	0.506	0.500	0.506
LDpred2
π	1	3e − 1	1e − 1	3e − 2	1e − 2	3e − 3	1e − 3	3e − 4	1e − 4	3e − 5	1e − 5
PRStuning	0.768	0.777	0.767	0.781	0.767	0.837	0.890	0.919	0.875	0.915	0.926
Testing	0.780	0.787	0.793	0.785	0.771	0.818	0.846	0.859	0.838	0.856	0.861

We randomly selected 80% of individuals as training data and the rest as the testing data. The data from the 1KG were used as the reference panel. For C+T, LDpred, and LDpred2, respectively, the correlation values ρ_AUC reached 0.994, 0.998, 0.989, the relative difference values rd_AUC were 3.8%, 1.3%, 7.0%, and the sensitivity values of the tuned PRS model based on PRStuning were 80.6%, 74.8%, 85.3%. Sensitivity is calculated using the cutoff value selected by Youden’s J statistic.