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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%
  1. The rate of re-classification into low risk (< 20th percentile), intermediate risk (20–80th percentile), and high risk (> 80th percentile) due to phasing and imputation variability across all individuals included in this study (1447 EURs and 239 AFRs combined). Columns indicate the average individual-level imputation-based risk tier. Rows indicate the process-level imputation-based risk tier