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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%)
  1. Columns indicate the number and percentage of subjects in the population with percentile change in their PRS. EUR European, AFR African