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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