Table 2.
Mean predictive performance of the test set
| Population type | P value | SNPs | AUC | Sens | Spec | PPV | NPV | Gini | Log-loss | MSE |
| Japanese | <0.001 | 2211 | 0.78±0.01 | 0.73±0.05 | 0.72±0.04 | 0.29±0.02 | 0.94±0.01 | 0.57±0.02 | 1.06±0.80 | 0.18±0.14 |
| <1.0×10−4 | 587 | 0.77±0.01 | 0.71±0.01 | 0.71±0.02 | 0.28±0.01 | 0.94±0.00 | 0.54±0.02 | 0.73±0.07 | 0.14±0.01 | |
| <1.0×10−5 | 262 | 0.75±0.01 | 0.70±0.01 | 0.69±0.03 | 0.26±0.02 | 0.94±0.00 | 0.50±0.02 | 0.73±0.11 | 0.18±0.02 | |
| <1.0×10−6 | 153 | 0.77±0.01 | 0.72±0.03 | 0.69±0.04 | 0.27±0.02 | 0.94±0.00 | 0.54±0.01 | 0.64±0.03 | 0.18±0.01 | |
| <5.0×10−8 | 91 | 0.75±0.01 | 0.68±0.01 | 0.70±0.03 | 0.27±0.01 | 0.93±0.00 | 0.50±0.02 | 0.61±0.01 | 0.20±0.00 | |
| ≥0.990 | 4221 | 0.56±0.03 | 0.54±0.07 | 0.56±0.04 | 0.16±0.01 | 0.88±0.01 | 0.12±0.05 | 0.98±0.09 | 0.16±0.07 | |
| European | <0.001 | 5401 | 0.74±0.02 | 0.72±0.05 | 0.65±0.04 | 0.25±0.02 | 0.94±0.01 | 0.48±0.05 | 5.46±0.66 | 0.42±0.27 |
| <1.0×10−4 | 2755 | 0.76±0.02 | 0.72±0.04 | 0.69±0.04 | 0.27±0.02 | 0.94±0.01 | 0.52±0.04 | 3.60±1.62 | 0.61±0.28 | |
| <1.0×10−5 | 1704 | 0.79±0.01 | 0.74±0.03 | 0.72±0.04 | 0.30±0.02 | 0.95±0.01 | 0.59±0.03 | 0.63±0.05 | 0.12±0.02 | |
| <1.0×10−6 | 1192 | 0.78±0.01 | 0.72±0.04 | 0.71±0.04 | 0.29±0.02 | 0.94±0.01 | 0.57±0.03 | 0.72±0.12 | 0.13±0.04 | |
| <5.0×10−8 | 814 | 0.78±0.01 | 0.71±0.03 | 0.72±0.03 | 0.29±0.02 | 0.94±0.00 | 0.56±0.02 | 0.68±0.04 | 0.13±0.03 | |
| ≥0.990 | 4699 | 0.56±0.05 | 0.57±0.03 | 0.55±0.08 | 0.17±0.02 | 0.89±0.01 | 0.12±0.10 | 2.16±0.73 | 0.12±0.09 | |
| Multiethnic | <0.001 | 4732 | 0.77±0.01 | 0.72±0.05 | 0.70±0.04 | 0.27±0.02 | 0.94±0.01 | 0.54±0.02 | 2.39±1.61 | 0.29±0.34 |
| <1.0×10−4 | 2372 | 0.79±0.01 | 0.72±0.03 | 0.73±0.04 | 0.30±0.02 | 0.94±0.00 | 0.58±0.03 | 1.19±0.72 | 0.13±0.10 | |
| <1.0×10−5 | 1540 | 0.82±0.01 | 0.74±0.04 | 0.76±0.03 | 0.33±0.01 | 0.95±0.01 | 0.63±0.02 | 0.61±0.07 | 0.12±0.04 | |
| <1.0×10−6 | 1037 | 0.78±0.02 | 0.72±0.03 | 0.70±0.04 | 0.28±0.02 | 0.94±0.01 | 0.56±0.04 | 0.81±0.16 | 0.13±0.01 | |
| <5.0×10−8 | 723 | 0.79±0.01 | 0.74±0.03 | 0.71±0.03 | 0.29±0.02 | 0.95±0.00 | 0.58±0.03 | 0.75±0.02 | 0.15±0.03 | |
| ≥0.990 | 4965 | 0.56±0.01 | 0.56±0.02 | 0.56±0.04 | 0.17±0.01 | 0.89±0.01 | 0.12±0.03 | 0.98±0.09 | 0.11±0.07 |
Data are shown as the mean±SD.
The best model of each ethnicity is shown in bold.
AUC, area under the curve; MSE, mean square error; NPV, negative predictive value; PPV, positive predictive value; Sens, sensitivity; SNPs, single-nucleotide polymorphisms; Spec, specificity.