Table 2.
Summary of polygenic risk score (PRS) analyses using two P-value thresholds and two different GWAS datasets with and without markers in the APOE region.
| PRS constructed based on GWAS by Jansen et al.7 | PRS constructed based on GWAS by IGAP, 2013 | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Including APOE | Excluding APOE | Including APOE | Excluding APOE | |||||||||||||
| S1(P < 5E-8) | S5( < 0.05) | S1(P < 5E-8) | S5( < 0.05) | S1(P < 5E-8) | S5( < 0.05) | S1(P < 5E-8) | S5( < 0.05) | |||||||||
| Phenotype | r2 | P-value | r2 | P-value | r2 | P-value | r2 | P-value | r2 | P-value | r2 | P-value | r2 | P-value | r2 | P-value |
| AD | 3.09% | 8E-05 | 2.89% | 0.0002 | 1.22% | 0.0126 | 0.99% | 0.0244 | 2.98% | 0.0001 | 1.69% | 0.0034 | 0.78% | 0.0443 | 0.10% | 0.4745 |
| MCI | 0.12% | 0.3767 | 0.77% | 0.0249 | 0.07% | 0.4894 | 0.61% | 0.0449 | 0.51% | 0.0682 | 0.13% | 0.3537 | 0.49% | 0.0743 | 0.00% | 0.8764 |
| AMYLOIDstatus | 1.38% | 0.0004 | 1.01% | 0.0025 | 0.38% | 0.0643 | 0.04% | 0.5599 | 3.82% | 9E-09 | 2.95% | 3E-07 | 1.09% | 0.0018 | 0.34% | 0.0766 |
| Amyloid.MCI | 4.59% | 0.0008 | 5.82% | 0.0002 | 1.33% | 0.0684 | 0.87% | 0.1394 | 12.54% | 1E-07 | 7.45% | 2E-05 | 4.63% | 0.0008 | 0.82% | 0.1513 |
| Amyloid.NC | 0.83% | 0.1637 | 0.23% | 0.4657 | 0.20% | 0.4928 | 0.01% | 0.8786 | 2.45% | 0.0174 | 5.10% | 0.0008 | 0.24% | 0.4592 | 1.28% | 0.0866 |
| AB_Zscore | 1.20% | 0.0003 | 0.80% | 0.0031 | 0.27% | 0.0871 | 0.01% | 0.7683 | 2.61% | 7E-08 | 3.08% | 4E-09 | 0.39% | 0.0382 | 0.38% | 0.04 |
| Central_CSF_ratiodich | 3.86% | 2E-06 | 1.94% | 0.0007 | 1.49% | 0.0029 | 0.10% | 0.4414 | 5.87% | 9E-09 | 3.52% | 6E-06 | 1.58% | 0.0022 | 0.22% | 0.2439 |
| Local_AB42_Abnormal | 3.68% | 4E-06 | 1.13% | 0.0098 | 1.65% | 0.0019 | 0.02% | 0.7287 | 3.40% | 1E-05 | 1.66% | 0.0018 | 0.94% | 0.0184 | 0.01% | 0.7873 |
| Central_CSF_AB38 | 0.21% | 0.2273 | 0.00% | 0.8587 | 0.32% | 0.1305 | 0.01% | 0.7838 | 0.00% | 0.8816 | 0.28% | 0.1614 | 0.03% | 0.6416 | 0.33% | 0.1279 |
| Central_CSF_AB40 | 0.24% | 0.1805 | 0.01% | 0.7974 | 0.28% | 0.1514 | 0.05% | 0.5298 | 0.05% | 0.5418 | 0.44% | 0.0718 | 0.07% | 0.4874 | 0.36% | 0.106 |
| log_Central_CSF_AB4240ratio | 2.06% | 4E-05 | 1.68% | 0.0002 | 0.49% | 0.0453 | 0.07% | 0.4428 | 3.74% | 3E-08 | 2.55% | 5E-06 | 0.56% | 0.0323 | 0.05% | 0.5324 |
| log_Central_CSF_AB42 | 1.52% | 0.0005 | 0.52% | 0.0445 | 0.56% | 0.0373 | 0.01% | 0.8297 | 2.31% | 2E-05 | 2.17% | 4E-05 | 0.53% | 0.0425 | 0.25% | 0.1605 |
| Local_PTAU_Abnormal | 0.31% | 0.1602 | 0.03% | 0.662 | 0.06% | 0.5386 | 0.01% | 0.8148 | 0.69% | 0.0347 | 0.38% | 0.1192 | 0.19% | 0.2697 | 0.09% | 0.4424 |
| Local_TTAU_Abnormal | 0.93% | 0.0107 | 0.01% | 0.7505 | 0.56% | 0.0465 | 0.12% | 0.3625 | 0.82% | 0.0166 | 0.27% | 0.1644 | 0.17% | 0.267 | 0.04% | 0.5771 |
| Ptau_ASSAY_Zscore | 0.34% | 0.0909 | 0.00% | 0.9833 | 0.09% | 0.3922 | 0.05% | 0.5191 | 0.37% | 0.0806 | 0.08% | 0.4258 | 0.01% | 0.7755 | 0.01% | 0.8237 |
| Ttau_ASSAY_Zscore | 0.51% | 0.032 | 0.03% | 0.6082 | 0.23% | 0.1529 | 0.00% | 0.9666 | 0.09% | 0.3566 | 0.11% | 0.3269 | 0.03% | 0.5811 | 0.00% | 0.8676 |
Italicized values = nominally significant association.
r2 = variance explained; bold font = largest r2 (= most variance explained) for trait in question.
A full listing of results from these PRS analyses can be found in Supplementary righthandcolumns of Table 2 and bottom part of SupplementaryTable 19 (for Jansen et al. GWAS) and Supplementary Table 20 (for IGAP GWAS).