Table 3 The rate of risk tier re-classification due to imputation variability using quintile-based cutoffs
From: Genotype imputation and variability in polygenic risk score estimation
Risk tier | Beagle | Eagle+Minimac | SHAPEIT+Minimac | ||||||
|---|---|---|---|---|---|---|---|---|---|
< 20%tile | 20–80%tile | > 80%tile | < 20%tile | 20–80%tile | > 80%tile | < 20%tile | 20–80%tile | > 80%tile | |
PRSCAD (161) | |||||||||
 < 20%tile | 19.89% | 0.09% | 0% | 19.99% | 0% | 0% | 19.27% | 0.72% | 0% |
 20–80%tile | 0.04% | 59.90% | 0.09% | 0% | 60.01% | 0.01% | 0.48% | 58.88% | 0.64% |
 > 80%tile | 0% | 0.10% | 19.90% | 0% | 0.01% | 19.98% | 0% | 0.48% | 19.52% |
metaGRSCAD (1736608) | |||||||||
 < 20%tile | 19.88% | 0.11% | 0% | 19.98% | 0.01% | 0% | 19.47% | 0.51% | 0% |
 20–80%tile | 0.29% | 59.59% | 0.13% | 0.01% | 60% | 0% | 0.51% | 58.95% | 0.54% |
 > 80%tile | 0% | 0.09% | 19.92% | 0% | 0.01% | 19.99% | 0% | 0.50% | 19.50% |
GPSCAD (6238460) | |||||||||
 < 20%tile | 19.85% | 0.14% | 0% | 19.96% | 0.02% | 0% | 19.57% | 0.42% | 0% |
 20–80%tile | 0.08% | 59.76% | 0.17% | 0.03% | 60% | 0% | 0.59% | 58.93% | 0.48% |
 > 80%tile | 0% | 0.13% | 19.88% | 0% | 0% | 19.99% | 0% | 0.56% | 19.44% |