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Table 4 The rate of risk tier re-classification for high risk individuals due to phasing and imputation variability

From: Genotype imputation and variability in polygenic risk score estimation

Risk tier Beagle Eagle+Minimac SHAPEIT+Minimac
PRSCAD (161)
 < 5%tile 1.19% (− 1.13–3.51) 0% (0–0) 15.66% (7.84–23.48)
 < 10%tile 2.96% (0.4–5.51) 0% (0–0) 10.12% (5.56–14.68)
 < 15%tile 1.59% (0.04–3.13) 0% (0–0) 9.96% (6.26–13.67)
 < 20%tile 0.89% (− 0.11–1.9) 0% (0–0) 9.91% (6.7–13.12)
 > 80%tile 1.78% (0.37–3.19) 0.3% (− 0.28–0.88) 10% (6.81–13.19)
 > 85%tile 1.98% (0.26–3.69) 0% (0–0) 12.7% (8.59–16.81)
 > 90%tile 1.19% (− 0.45–2.83) 0% (0–0) 17.54% (11.84–23.24)
 > 95%tile 4.71% (0.2–9.21) 0% (0–0) 15.85% (7.95–23.76)
metaGRSCAD (1736608)
 < 5%tile 6.98% (1.59–12.36) 1.19% (− 1.13–3.51) 18.6% (10.38–26.83)
 < 10%tile 2.37% (0.07–4.66) 0% (0–0) 6.67% (2.86–10.47)
 < 15%tile 2.37% (0.5–4.25) 0.79% (− 0.3–1.88) 12.94% (8.82–17.06)
 < 20%tile 3.82% (1.79–5.86) 0.3% (− 0.28–0.88) 8.9% (5.86–11.94)
 > 80%tile 2.66% (0.95–4.38) 0% (0–0) 9.76% (6.6–12.93)
 > 85%tile 4.72% (2.12–7.33) 0% (0–0) 12.11% (8.11–16.11)
 > 90%tile 6.43% (2.76–10.11) 0% (0–0) 6.06% (2.42–9.7)
 > 95%tile 2.38% (− 0.88–5.64) 0% (0–0) 9.52% (3.25–15.8)
GPSCAD (6238460)
 < 5%tile 5.88% (0.88–10.88) 0% (0–0) 13.25% (5.96–20.55)
 < 10%tile 2.38% (0.08–4.69) 0.59% (− 0.56–1.75) 7.78% (3.72–11.85)
 < 15%tile 0.79% (− 0.3–1.88) 0% (0–0) 9.92% (6.23–13.61)
 < 20%tile 1.49% (0.19–2.78) 0.3% (− 0.28–0.88) 10% (6.81–13.19)
 > 80%tile 2.37% (0.75–3.99) 0% (0–0) 8.33% (5.38–11.29)
 > 85%tile 1.97% (0.26–3.68) 0% (0–0) 6.48% (3.41–9.55)
 > 90%tile 2.37% (0.07–4.66) 0% (0–0) 5.99% (2.39–9.59)
 > 95%tile 1.18% (− 1.12–3.47) 0% (0–0) 10.59% (4.05–17.13)
  1. The rate of individuals re-classified from high risk tiers due to imputation variability across all individuals included in this study (1447 EURs and 239 AFRs combined). An individual is considered re-classified if at least two imputation replicates produce a different risk tier than the WGS-based ground truth. Values in parenthesis present the 95% confidence interval