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. 2015 Oct 21;138(12):3673–3684. doi: 10.1093/brain/awv268

Table 3.

Predictive accuracy for 3049 Alzheimer’s disease cases versus 1554 controls

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.