table 1.

Mean Performance Metrics for 1-Year Risk Prediction of CAD

	All			Low-Risk
Model	AUROC	PPV	NPV	AUROC	PPV	NPV
BioMe
Age + sex	0.70 ± 0.04	0.68 ± 0.04	0.69 ± 0.04	0.64 ± 0.12	0.60 ± 0.17	0.63 ± 0.13
Age + sex + eth	0.79 ± 0.04	0.70 ± 0.04	0.72 ± 0.05	0.67 ± 0.11	0.62 ± 0.11	0.64 ± 0.13
Age + sex + 10 PC	0.82 ± 0.03	0.75 ± 0.04	0.76 ± 0.04	0.69 ± 0.12	0.66 ± 0.12	0.65 ± 0.12
PRS	0.83 ± 0.03	0.76 ± 0.05	0.76 ± 0.04	0.71 ± 0.11	0.66 ± 0.12	0.66 ± 0.11
PCE	0.82 ± 0.04	0.74 ± 0.04	0.73 ± 0.05	0.67 ± 0.13	0.61 ± 0.11	0.63 ± 0.15
PCE + PRS	0.83 ± 0.04	0.76 ± 0.04	0.74 ± 0.05	0.69 ± 0.13	0.63 ± 0.13	0.63 ± 0.13
EHR	0.94 ± 0.02	0.88 ± 0.04	0.85 ± 0.04	0.87 ± 0.07	0.81 ± 0.10	0.78 ± 0.10
EHR + PRS	0.95 ± 0.02	0.88 ± 0.04	0.85 ± 0.04	0.88 ± 0.07	0.81 ± 0.09	0.80 ± 0.09
EHR + PCE	0.94 ± 0.02	0.88 ± 0.03	0.85 ± 0.04	0.86 ± 0.07	0.78 ± 0.10	0.77 ± 0.10
EHR + PCE + PRS	0.94 ± 0.02	0.88 ± 0.04	0.85 ± 0.04	0.88 ± 0.07	0.79 ± 0.11	0.79 ± 0.10
UK Biobank
Age + sex	0.74 ± 0.02	0.67 ± 0.02	0.68 ± 0.02	0.59 ± 0.02	0.57 ± 0.01	0.57 ± 0.03
Age + sex + eth	0.74 ± 0.02	0.67 ± 0.02	0.68 ± 0.02	0.60 ± 0.03	0.57 ± 0.02	0.58 ± 0.03
Age + sex + 10 PC	0.69 ± 0.02	0.58 ± 0.04	0.68 ± 0.02	0.57 ± 0.04	0.50 ± 0.02	0.81 ± 0.02
PCE	0.79 ± 0.02	0.69 ± 0.02	0.75 ± 0.03	0.69 ± 0.01	0.62 ± 0.02	0.65 ± 0.03
EHR	0.88 ± 0.01	0.92 ± 0.02	0.73 ± 0.02	0.80 ± 0.04	0.68 ± 0.10	0.87 ± 0.02

Values are mean ± SD across 100 iterations. Performance metrics for models are shown for BioMe and UK Biobank. Columns correspond to performance metrics in test set from BioMe Biobank and validation set from UK Biobank. Rows correspond to the model being tested.

AUROC = area under the receiver-operating characteristic curve; EHR = electronic health records; eth = ethnicity; NPV = negative predicted value; PC = principal components; PCE = pooled cohort equations; PRS = polygenic risk score; PPV = positive predicted value.