Table 3 

Prediction Results for three test sets. 

No. of genes for prediction 
Ttest (Pvalue) 
Sensitivity (%) 
Specificity (%) 
PPV (%) 
NPV (%) 
Youden index 



56 gene model 



FH2 
56 
0.011 
70.0 
84.6 
77.8 
78.6 
0.55 
FH3 
56 
0.010 
80.0 
100 
100 
0.83 
0.8 
ATHRO1 
56 
0.019 
71.4 
71.4 
71.4 
71.4 
0.43 


COXEN model 



48 
0.0024 
70.0 
92.3 
87.5 
80.0 
0.62 

6 
1.5e10 
100 
100.0 
100.0 
100 
1.00 

25 
0.010 
78.6 
66.7 
68.8 
76.9 
0.45 



Data sets FH2, FH3, and ATHERO1 were used to evaluate the classification performance of our atherosclerosis prediction model. We tested if the predicted risk of atherosclerosis could statistically discriminate familial hypercholesterolemia or general atherosclerosis patients with normal people in these test sets. The statistical significance of the difference in predicted scores (COXEN SCORE) was evaluated using the twosample ttest between patients and normal groups. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were also calculated. 

Cheng et al. BMC Medical Genomics 2012 5:2 doi:10.1186/1755879452 