Table 2 Performance evaluation of PRSs derived from different approaches in validation datasets

GWAS-reported

EUR

140

0.511/0.510

1.04 (0.95, 1.14)

0.432

0.629/0.638

1.65 (1.51, 1.81)

1.49E−28

EAS

37

0.577/0.580

1.33 (1.21, 1.46)

2.01E−09

0.513/0.506

1.02 (0.94, 1.11)

0.567

C+T

5.00E−08 (0.001)

38

0.569/0.573

1.29 (1.18, 1.42)

6.73E−08

0.579/0.583

1.33 (1.23, 1.45)

1.77E−11

5.00E−06 (0.001)

88

0.569/0.575

1.30 (1.18, 1.43)

3.30E−08

0.589/0.597

1.39 (1.28, 1.51)

4.02E−14

5.00E−04 (0.001)

784

0.591/0.597

1.44 (1.31, 1.58)

5.39E−14

0.559/0.567

1.27 (1.16, 1.38)

3.51E−08

0.05 (0.001)

7128

0.611/0.618

1.52 (1.38, 1.68)

1.52E−17

0.556/0.556

1.23 (1.13, 1.33)

1.65E−06

5.00E−08 (0.01)

39

0.570/0.573

1.29 (1.18, 1.42)

8.02E−08

0.572/0.574

1.30 (1.20, 1.42)

5.96E−10

5.00E−06 (0.01)

92

0.571/0.577

1.30 (1.18, 1.42)

4.54E−08

0.583/0.590

1.35 (1.24, 1.47)

4.36E−12

5.00E−04 (0.01)

854

0.588/0.593

1.42 (1.30, 1.57)

2.62E−13

0.558/0.564

1.25 (1.15, 1.36)

1.04E−07

0.05 (0.01)

13,989

0.587/0.592

1.37 (1.25, 1.50)

4.12E−11

0.555/0.553

1.21 (1.12, 1.32)

4.89E−06

5.00E−08 (0.1)

48

0.573/0.577

1.31 (1.20, 1.44)

1.02E−08

0.581/0.581

1.33 (1.22, 1.44)

3.99E−11

5.00E−06 (0.1)

116

0.579/0.584

1.34 (1.22, 1.47)

7.91E−10

0.592/0.597

1.39 (1.28, 1.51)

3.42E−14

5.00E−04 (0.1)

992

0.597/0.602

1.46 (1.33, 1.61)

6.02E−15

0.573/0.577

1.31 (1.20, 1.42)

3.22E−10

0.05 (0.1)

27,032

0.604/0.608

1.52 (1.38, 1.68)

7.05E−18

0.568/0.573

1.29 (1.19, 1.40)

2.61E−09

LDpred

1

883,144

0.611/0.616

1.55 (1.40, 1.70)

8.25E−19

0.560/0.567

1.27 (1.17, 1.38)

2.13E−08

0.3

883,144

0.612/0.617

1.56 (1.41, 1.71)

3.15E−19

0.560/0.567

1.28 (1.18, 1.39)

8.60E−09

0.1

883,144

0.614/0.619

1.58 (1.43, 1.74)

3.26E−20

0.567/0.574

1.31 (1.20, 1.42)

4.61E−10

0.03

883,144

0.621/0.626

1.64 (1.48, 1.80)

6.87E−23

0.586/0.595

1.39 (1.27, 1.51)

6.45E−14

0.01

883,144

0.633/0.638

1.68 (1.52, 1.85)

7.86E−25

0.602/0.608

1.47 (1.35, 1.60)

2.04E−18

0.003

883,144

0.495/0.491

0.98 (0.89, 1.07)

0.627

0.514/0.513

1.02 (0.94, 1.11)

0.663

0.001

883,144

0.508/0.509

1.04 (0.95, 1.14)

0.436

0.491/0.490

0.95 (0.88, 1.04)

0.257

3.00E−04

883,144

0.499/0.499

0.99 (0.91, 1.09)

0.885

0.493/0.491

0.98 (0.91, 1.07)

0.704

1.00E−04

883,144

0.487/0.489

0.94 (0.86, 1.03)

0.202

0.510/0.508

1.04 (0.96, 1.13)

0.343

3.00E−05

883,144

0.494/0.498

0.98 (0.89, 1.07)

0.670

0.501/0.507

1.03 (0.95, 1.12)

0.464

1.00E−05

883,144

0.480/0.482

0.95 (0.87, 1.04)

0.277

0.505/0.500

1.02 (0.94, 1.11)

0.653

Lassosum

Optimal

5984

0.606/0.610

1.51 (1.37, 1.66)

4.53E−17

0.601/0.605

1.45 (1.33, 1.58)

2.12E−17

LDpred2

Auto

890,687

0.570/0.573

1.30 (1.19, 1.43)

2.36E−08

0.557/0.563

1.24 (1.14, 1.35)

3.19E−07

PRS-CSx^#

Auto

1,145,689

0.639/0.646

1.73 (1.56, 1.91)

7.19E−27

0.602/0.608

1.48 (1.36, 1.62)

5.18E−19