Table 2 The accuracy of PRS models for predicting ANA positive to SLE progressions in the All of Us biobank
Model | \({R}^{2}\) | AUPRC | AUC |
|---|---|---|---|
CC-Lassosum | 0.033 (0.015, 0.052) | 0.112 (0.088, 0.15) | 0.568 (0.506, 0.628) |
CC-LDpred2 | 0.01 (0, 0.021) | 0.096 (0.077, 0.123) | 0.540 (0.482, 0.596) |
CC-PRS-CS | 0.032 (0.014, 0.05) | 0.11 (0.087, 0.146) | 0.566 (0.508, 0.625) |
PROG-Lassosum | 0.001 (−0.002, 0.004) | 0.093 (0.076, 0.127) | 0.519 (0.465, 0.575) |
PROG-LDpred2 | 0.019 (0.005, 0.033) | 0.096 (0.079, 0.12) | 0.554 (0.498, 0.606) |
PROG-PRS-CS | 0.01 (0, 0.021) | 0.095 (0.078, 0.119) | 0.543 (0.488, 0.592) |
MTAG-Lassosum | 0.001 (−0.002, 0.003) | 0.091 (0.074, 0.116) | 0.516 (0.455, 0.573) |
MTAG-LDpred2 | 0.005 (−0.002, 0.012) | 0.09 (0.075, 0.11) | 0.533 (0.479, 0.583) |
MTAG-PRS-CS | 0.003 (−0.003, 0.008) | 0.091 (0.076, 0.113) | 0.528 (0.471, 0.576) |
GPS-Lassosum | 0.044 (0.023, 0.065) | 0.124 (0.091, 0.171) | 0.568 (0.511, 0.622) |
GPS-LDpred2 | 0.037 (0.018, 0.056) | 0.117 (0.089, 0.167) | 0.566 (0.513, 0.623) |
GPS-PRS-CS | 0.042 (0.021, 0.062) | 0.119 (0.09, 0.163) | 0.566 (0.51, 0.623) |
TL-PRS-Lassosum | 0.028 (0.011, 0.044) | 0.102 (0.084, 0.131) | 0.561 (0.507, 0.612) |
TL-PRS-LDpred2 | 0.007 (−0.002, 0.016) | 0.093 (0.077, 0.118) | 0.527 (0.477, 0.578) |
TL-PRS-PRS-CS | 0.027 (0.011, 0.044) | 0.100 (0.083, 0.126) | 0.558 (0.509, 0.605) |
STACKING-Lassosum | 0.034 (0.016, 0.053) | 0.111 (0.088, 0.148) | 0.570 (0.51, 0.63) |
STACKING-LDpred2 | 0.028 (0.011, 0.046) | 0.103 (0.082, 0.131) | 0.558 (0.499, 0.611) |
STACKING-PRS-CS | 0.039 (0.019, 0.059) | 0.112 (0.089, 0.149) | 0.569 (0.51, 0.626) |
MVL | 0.0046 (−0.0025, 0.012) | 0.090 (0.075, 0.113) | 0.529 (0.476, 0.579) |
