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)

We report the Nagelkerke’s $R^{\mathit{2}}$, AUPRC (area under the precision recall curve), and AUC (area under the receiver operating characteristic curve). The 95% confidence intervals for the estimates are listed in the parenthesis. The top two methods for each metric are displayed in bold and italic font.