Table 2:
The performance metrics of the GPS in the testing cohorts meta-analyzed by ancestry. For performance testing in individual cohorts, please refer to Supplemental Tables 4–7.
| Meta-analysis | Case/control | OR per SD (95% CI), P-value | AUC (Crude) | PRS Threshold | Odds ratio (95% CI), P-value |
|---|---|---|---|---|---|
| European (3 cohorts) | 14,201/82,849 | 1.46 (1.43-1.48), P<1.00E-300 | 0.81 (0.62) | Top 20% vs. other 80% | 2.30 (2.17-2.44), P=1.65E-174 |
| Top 10% vs. other 90% | 2.59 (2.40-2.78), P=1.27E-142 | ||||
| Top 5% vs. other 95% | 2.92 (2.65-3.21), P=2.64E-104 | ||||
| Top 2% vs. other 98% | 3.60 (3.11-4.17), P=4.26E-66 | ||||
| Top 1% vs. other 99% | 4.46 (3.66-5.44), P=7.82E-50 | ||||
|
| |||||
| African (6 cohorts) | 4,268/10,276 | 1.32 (1.26-1.38), P=1.78E-33 | 0.78 (0.57) | Top 20% vs. other 80% | 1.65 (1.49-1.82), P=1.17E-22 |
| Top 10% vs. other 90% | 1.84 (1.61-2.09), P=9.26E-20 | ||||
| Top 5% vs. other 95% | 2.06 (1.72-2.47), P=2.11E-15 | ||||
| Top 2% vs. other 98% | 2.66 (2.01-3.51), P= 4.93E-12 | ||||
| Top 1% vs. other 99% | 3.51 (2.37-5.22), P=4.21E-10 | ||||
|
| |||||
| Latinx (2 cohorts) | 1,386/2,239 | 1.42 (1.29-1.57), P=4.56E-12 | 0.88 (0.62) | Top 20% vs. other 80% | 1.88 (1.50-2.37), P=5.46E-08 |
| Top 10% vs. other 90% | 2.26 (1.66-3.06), P=1.56E-07 | ||||
| Top 5% vs. other 95% | 2.67 (1.75-4.07), P=4.96E-06 | ||||
| Top 2% vs. other 98% | 4.93 (2.46-9.89), P=6.69E-06 | ||||
| Top 1% vs. other 99% | 6.61 (2.46-17.75), P=1.77E-04 | ||||
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| |||||
| Asian (4 cohorts) | 392/8,233 | 1.68 (1.45-2.06), P=7.11E-13 | 0.91 (0.61) | Top 20% vs. other 80% | 2.42 (1.81-2.27), P=4.39E-09 |
| Top 10% vs. other 90% | 2.95 (2.06-4.20), P=2.43E-09 | ||||
| Top 5% vs. other 95% | 3.56 (2.26-5.60), P=4.09E-08 | ||||
| Top 2% vs. other 98% | 3.81 (1.91-7.59), P=1.35E-04 | ||||
| Top 1% vs. other 99% | 8.46 (3.70-19.3), P=4.00E-07 | ||||
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| |||||
| All 15 cohorts | 20,247/103,597 | 1.44 (1.42-1.47), P<1.00E-300 | 0.81 (0.61) | Top 20% vs. other 80% | 2.23 (2.11-2.35), P=8.02E-195 |
| Top 10% vs. other 90% | 2.31 (2.17-2.45), P=2.75E-168 | ||||
| Top 5% vs. other 95% | 2.58 (2.39-2.79), P=2.02E-123 | ||||
| Top 2% vs. other 98% | 3.26 (2.89-3.67), P=3.37E-84 | ||||
| Top 1% vs. other 99% | 4.61 (3.84-5.53), P=1.14E-60 | ||||
OR: Odds ratio for the model adjusted for age, sex, diabetes, principal components of ancestry and genotyping array or clinical site; SD: standard deviation of the GPS distribution in controls; AUC: area under the receiver-operator curve for the model adjusted for age, sex, diabetes, principal components of ancestry and genotyping array or clinical site (crude: AUC for GPS alone without any covariates).