table 2.
Mean Net Reclassification Improvement for 1-Year Risk Prediction of CAD
| All | Low-Risk | |||||
|---|---|---|---|---|---|---|
|
|
|
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| Model | Overall | Cases | Control Subjects | Overall | Cases | Control Subjects |
|
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| BioMe | ||||||
| Age + sex | −9.6 ± 7.8 | −1.8 ± 7.0 | −7.8 ± 7.1 | −0.9 ± 28.2 | 4.2 ± 26.1 | −5.1 ± 23.3 |
| Age + sex + eth | −4.6 ± 7.2 | 1.1 ± 6.4 | −5.7 ± 5.7 | 2.1 ± 26.9 | 4.4 ± 24.3 | −2.3 ± 19.4 |
| Age + sex + 10 PC | 3.4 ± 7.7 | 4.4 ± 6.3 | −1.0 ± 6.1 | 5.1 ± 24.1 | 0.7 ± 23.4 | 4.4 ± 19.2 |
| PRS | 3.8 ± 7.7 | 3.7 ± 6.4 | 0.2 ± 6.2 | 6.9 ± 26.6 | 2.2 ± 24.0 | 4.7 ± 19.6 |
| PCE + PRS | 2.7 ± 5.5 | 0.6 ± 5.2 | 2.1 ± 4.7 | 4.2 ± 23.6 | 4.2 ± 23.0 | 0.0 ± 17.2 |
| EHR | 25.8 ± 8.5 | 12.4 ± 7.5 | 13.4 ± 5.6 | 34.4 ± 27.1 | 14.0 ± 23.5 | 20.4 ± 18.4 |
| EHR + PRS | 26.1 ± 8.7 | 12.4 ± 7.7 | 13.7 ± 5.1 | 35.6 ± 26.9 | 15.6 ± 23.6 | 19.7 ± 17.3 |
| EHR + PCE | 25.1 ± 7.7 | 12.2 ± 7.0 | 12.9 ± 5.1 | 31.3 ± 26.9 | 14.8 ± 23.0 | 18.5 ± 18.0 |
| EHR + PCE + PRS | 25.6 ± 7.7 | 12.7 ± 7.1 | 12.9 ± 4.8 | 33.7 ± 25.5 | 16.1 ± 22.0 | 17.6 ± 17.8 |
| UK Biobank | ||||||
| Age + sex | −7.9 ± 2.8 | −8.9 ± 4.0 | 1.0 ± 4.1 | −13.0 ± 4.7 | −8.8 ± 11.4 | −4.2 ± 8.9 |
| Age + sex + eth | −7.7 ± 2.7 | −8.3 ± 3.4 | 0.6 ± 3.8 | −12.8 ± 6.0 | −6.8 ± 11.0 | −6.0 ± 8.4 |
| Age + sex + 10 PC | −15.1 ± 3.8 | −35.4 ± 4.7 | 20.3 ± 3.7 | −38.3 ± 45.2 | −66.4 ± 11.2 | 27.6 ± 43.5 |
| EHR | 15.2 ± 4.1 | −13.5 ± 4.7 | 28.7 ± 3.9 | 9.3 ± 53.5 | −14.6 ± 14.7 | 24.1 ± 49.3 |
Values are mean ± across 100 iterations. Performance metrics for models are shown for BioMe and UK Biobank. Columns correspond to overall and by-class Net Reclassification Improvement in test set from BioMe Biobank and validation set from UK Biobank. Rows correspond to the model being tested.
Abbreviations as in Table 1.