Table 3.
Model | NSNPs | Sensitivity | Specificity | AUC | AUC | Improve over APOE | Improve over APOE and GWA study | Hosmer-Lemeshow test |
---|---|---|---|---|---|---|---|---|
95% CI | P-value* | |||||||
ε4 | 1 | 0.593 | 0.746 | 0.678 | 0.66–0.69 | - | - | 0.987 |
ε4 + ε2 | 2 | 0.593 | 0.746 | 0.688 | 0.67–0.70 | - | - | 0.969 |
ε4 + ε2 + sex + age | 2 | 0.669 | 0.662 | 0.717 | 0.70–0.73 | 8.5 × 10−13 | - | 0.067 |
ε4 + ε2 + 20 GWAS SNPs | 22 | 0.666 | 0.666 | 0.715 | 0.70–0.73 | 2.7 × 10−12 | - | 0.234 |
ε4 + ε2 + 20 GWAS SNPs + PS P < 0.0001 | 130 | 0.669 | 0.669 | 0.717 | 0.70–0.73 | 2.5 × 10−14 | 0.048 | 0.218 |
ε4 + ε2 + 20 GWAS SNPs + PS P < 0.001 | 549 | 0.668 | 0.668 | 0.720 | 0.71–0.74 | 2.8 × 10−16 | 0.0082 | 0.415 |
ε4 + ε2 + 20 GWAS SNPs + PS P < 0.01 | 3388 | 0.672 | 0.672 | 0.729 | 0.71–0.74 | 1.1 × 10−21 | 9.5 × 10−6 | 0.855 |
ε4 + ε2 + 20 GWAS SNPs + PS P < 0.05 | 13273 | 0.677 | 0.677 | 0.738 | 0.72–0.75 | 7.4 × 10−27 | 3.6 × 10−9 | 0.633 |
ε4 + ε2 + 20 GWAS SNPs + PS P < 0.1 | 23676 | 0.682 | 0.682 | 0.740 | 0.73–0.76 | 3.5 × 10−28 | 5.9 × 10−10 | 0.575 |
ε4 + ε2 + 20 GWAS SNPs + PS P < 0.2 | 42273 | 0.683 | 0.683 | 0.743 | 0.73–0.76 | 1.5 × 10−29 | 3.6 × 10−11 | 0.211 |
ε4 + ε2 + 20 GWAS SNPs + PS P < 0.3 | 58963 | 0.684 | 0.683 | 0.744 | 0.73–0.76 | 2.0 × 10−29 | 3.9 × 10−11 | 0.139 |
ε4 + ε2 + 20 GWAS SNPs + PS P < 0.4 | 73941 | 0.684 | 0.684 | 0.744 | 0.73–0.76 | 1.1 × 10−29 | 2.1 × 10−11 | 0.213 |
ε4 + ε2 + 20 GWAS SNPs + PS P < 0.5 | 87605 | 0.686 | 0.686 | 0.745 | 0.73–0.76 | 7.2 × 10−30 | 1.3 × 10−11 | 0.225 |
ε4 + ε2 + 20 GWAS SNPs + PS P < 0.6 | 99724 | 0.685 | 0.685 | 0.745 | 0.73–0.76 | 4.4 × 10−30 | 9.4 × 10−12 | 0.155 |
ε4 + ε2 + 20 GWAS SNPs + PS P < 0.7 | 110431 | 0.685 | 0.685 | 0.745 | 0.73–0.76 | 1.0 × 10−29 | 1.7 × 10−11 | 0.076 |
ε4 + ε2 + 20 GWAS SNPs + PS P < 0.8 | 119616 | 0.683 | 0.683 | 0.745 | 0.73–0.76 | 6.2 × 10−30 | 1.2 × 10−11 | 0.095 |
ε4 + ε2 + 20 GWAS SNPs + PS P < 0.9 | 127585 | 0.684 | 0.684 | 0.745 | 0.73–0.76 | 6.3 × 10−30 | 1.2 × 10−11 | 0.185 |
ε4 + ε2 + 20 GWAS SNPs + PS P < 0.5 + age + sex | 87605 | 0.704 | 0.703 | 0.782 | 0.77–0.80 | 1.9 × 10−57 | 6.5 × 10−33 | 0.829 |
* Non-significant Hosmer-Lemeshow test P-value indicates that the model is correctly specified. The polygenic scores (PS) were constructed using independent SNPs associated with Alzheimer’s disease in IGAP.noGERAD at different significance levels (Model column), excluding APOE and 20 GWA study regions (Supplementary Table 2). Numbers of SNPs participating in the predictive model are given in column SNPs.