Table 3.
Haplotype frequencies in six human cohorts (haplotypes with f > 0.001). AD/MCI vs CT:GGATC (last column) represents the association of the haplotype with AD when compared to most common European haplotype (Fisher’s exact test); haplotypes with zero frequencies are excluded from analysis
| Haplotype | # added CG (positions) | APOE Allele | 1000G | ADNI | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Afr | Asian | Eur | AD | MCI | CT | AD vs CT:GGATC P value | MCI vs CT:GGATC P value | |||
| G G G CC | 3 (1,4,5) | ε4 | 0.292 | 0.0035 | 0.0205 | 0.0984 | 0.05 | 0.0371 | 1.6e-5 | 0.1975 |
| C G G T C | 1 (5) | ε3 | 0.13 | 0.628 | 0.363 | 0.268 | 0.354 | 0.379 | 1 | 0.7382 |
| G G A T C | 2 (1,5) | ε3 | 0.286 | 0.191 | 0.423 | 0.276 | 0.346 | 0.389 | NA | |
| G G G T C | 2 (1,5) | ε3 | 0.208 | 0.0175 | 0.00685 | 0.0137 | 0.023 | 0.0234 | 0.7979 | 0.8491 |
| G G G T T | 1(1) | ε2 | 0.0811 | 0.0752 | 0.0616 | 0.0219 | 0.0581 | 0.0703 | 0.039 | 0.8065 |
| G A G C C | 3 (1,4,5) | ε4 | 0 | 0.0839 | 0.119 | 0.309 | 0.165 | 0.0977 | 2e-13 | 0.001 |
| G G A T T | 1 (1) | ε2 | 0.0027 | 0 | 0 | 0 | 0 | 0 | ||
| C G A T C | 1 (5) | ε3 | 0 | 0.00175 | 0 | 0 | 0 | 0 | ||
| C G G T T | 0 | ε2 | 0 | 0 | 0.00411 | 0 | 0 | 0 | ||
| G A G C T | 2 (1,4) | ε3 | 0 | 0 | 0.00137 | 0 | 0 | 0 | ||
| G A G T C | 2 (1,5) | ε3 | 0 | 0 | 0 | 0.00273 | 0.00135 | 0 | ||
| C G G C C | 2 (4,5) | ε4 | 0 | 0 | 0 | 0.0082 | 0 | 0.00391 | 0.3419 | |
| C A G C C | 2 (4,5) | ε4 | 0 | 0 | 0 | 0.00273 | 0.00135 | 0 | ||
| G G A C C | 3 (1,4,5) | ε4 | 0 | 0 | 0 | 0 | 0.00135 | 0 | ||
| Total haplotypes | 370 | 572 | 730 | 366 | 740 | 512 | ||||
| Sample size | 185 | 286 | 365 | 183 | 370 | 256 | ||||