Table 2 The distribution of CAD risk score percentile changes caused by three different imputation processes
From: Genotype imputation and variability in polygenic risk score estimation
Percentile change | Beagle | Eagle+Minimac | SHAPEIT+Minimac | ||||||
|---|---|---|---|---|---|---|---|---|---|
EUR | AFR | All | EUR | AFR | All | EUR | AFR | All | |
PRSCAD (161) | |||||||||
 ≤ 1%tile | 1247 (86.18%) | 163 (68.2%) | 1410 (83.63%) | 1437 (99.31%) | 236 (98.74%) | 1673 (99.23%) | 259 (17.9%) | 5 (2.09%) | 264 (15.66%) |
 > 1%tile | 200 (13.82%) | 76 (31.8%) | 276 (16.37%) | 10 (0.69%) | 3 (1.26%) | 13 (0.77%) | 1188 (82.1%) | 234 (97.91%) | 1422 (84.34%) |
 > 5%tile | 21 (1.45%) | 5 (2.09%) | 26 (1.54%) | 7 (0.48%) | 1 (0.42%) | 8 (0.47%) | 331 (22.87%) | 168 (70.29%) | 499 (29.6%) |
 > 10%tile | 2 (0.14%) | 0 (0%) | 2 (0.12%) | 1 (0.07%) | 0 (0%) | 1 (0.06%) | 68 (4.7%) | 87 (36.4%) | 155 (9.19%) |
 > 20%tile | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 3 (0.21%) | 10 (4.18%) | 13 (0.77%) |
metaGRSCAD (1736608) | |||||||||
 ≤ 1%tile | 940 (64.96%) | 106 (44.35%) | 1046 (62.04%) | 1418 (98%) | 229 (95.82%) | 1647 (97.69%) | 153 (10.57%) | 13 (5.44%) | 166 (9.85%) |
 > 1%tile | 507 (35.04%) | 133 (55.65%) | 640 (37.96%) | 29 (2%) | 10 (4.18%) | 39 (2.31%) | 1294 (89.43%) | 226 (94.56%) | 1520 (90.15%) |
 > 5%tile | 12 (0.83%) | 2 (0.84%) | 14 (0.83%) | 5 (0.35%) | 1 (0.42%) | 6 (0.36%) | 277 (19.14%) | 154 (64.44%) | 431 (25.56%) |
 > 10%tile | 2 (0.14%) | 0 (0%) | 2 (0.12%) | 0 (0%) | 0 (0%) | 0 (0%) | 8 (0.55%) | 42 (17.57%) | 50 (2.97%) |
 > 20%tile | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
GPSCAD (6238460) | |||||||||
 ≤ 1%tile | 1289 (89.08%) | 191 (79.92%) | 1480 (87.78%) | 1429 (98.76%) | 233 (97.49%) | 1662 (98.58%) | 328 (22.67%) | 20 (8.37%) | 348 (20.64%) |
 > 1%tile | 158 (10.92%) | 48 (20.08%) | 206 (12.22%) | 18 (1.24%) | 6 (2.51%) | 24 (1.42%) | 1119 (77.33%) | 219 (91.63%) | 1338 (79.36%) |
 > 5%tile | 26 (1.8%) | 0 (0%) | 26 (1.54%) | 2 (0.14%) | 0 (0%) | 2 (0.12%) | 239 (16.52%) | 69 (28.87%) | 308 (18.27%) |
 > 10%tile | 12 (0.83%) | 0 (0%) | 12 (0.71%) | 0 (0%) | 0 (0%) | 0 (0%) | 56 (3.87%) | 9 (3.77%) | 65 (3.86%) |
 > 20%tile | 2 (0.14%) | 0 (0%) | 2 (0.12%) | 0 (0%) | 0 (0%) | 0 (0%) | 6 (0.41%) | 1 (0.42%) | 7 (0.42%) |