Table 1 Performances of Mondrian cross-conformal prediction at an error of 0.05 on various genetic architecture by simulation (proportion of discovery set for GWAS is 0.5).

From: Translating polygenic risk scores for clinical use by estimating the confidence bounds of risk prediction

Heritability

Polygenicity

Prevalence

AUC (95% CI)

PPV (95% CI)

NPV (95% CI)

Coverage

0.3

0.001

0.01

0.84 (0.80–0.88)

0.48 (0.44–0.53)

0.96 (0.94–0.98)

0.18

0.05

0.81 (0.79–0.84)

0.76 (0.73–0.80)

0.81 (0.77–0.84)

0.22

0.2

0.76 (0.73–0.79)

0.75 (0.72–0.81)

0.67 (0.61–0.72)

0.17

0.01

0.01

0.78 (0.71–0.84)

0.25 (0.19–0.35)

0.97 (0.95–0.99)

0.16

0.05

0.75 (0.71–0.79)

0.61 (0.57–0.65)

0.82 (0.79–0.85)

0.18

0.2

0.73 (0.70–0.77)

0.69 (0.66–0.73)

0.74 (0.71–0.78)

0.17

0.1

0.01

0.67 (0.58–0.76)

0.18 (0.13–0.33)

0.95 (0.92–0.99)

0.12

0.05

0.67 (0.62–0.71)

0.57 (0.52–0.63)

0.74 (0.70–0.78)

0.14

0.2

0.59 (0.55–0.64)

0.65 (0.59–0.73)

0.56 (0.53–0.61)

0.12

0.2

0.01

0.68 (0.60–0.76)

0.24 (0.20–0.29)

0.94 (0.91–0.97)

0.11

0.05

0.70 (0.65–0.74)

0.61 (0.57–0.65)

0.76 (0.72–0.80)

0.15

0.2

0.62 (0.58–0.67)

0.65 (0.60–0.69)

0.62 (0.58–0.66)

0.16

0.5

0.001

0.01

0.91 (0.89–0.94)

0.57 (0.52–0.61)

0.98 (0.97–0.99)

0.32

0.05

0.88 (0.86–0.90)

0.81 (0.79–0.84)

0.88 (0.86–0.90)

0.30

0.2

0.83 (0.80–0.85)

0.82 (0.79–0.84)

0.78 (0.75–0.81)

0.24

0.01

0.01

0.85 (0.81–0.90)

0.39 (0.34–0.44)

0.98 (0.96–0.99)

0.23

0.05

0.84 (0.82–0.87)

0.72 (0.69–0.76)

0.88 (0.86–0.90)

0.26

0.2

0.80 (0.77–0.82)

0.77 (0.74–0.80)

0.79 (0.76–0.82)

0.21

0.1

0.01

0.75 (0.69–0.81)

0.28 (0.24–0.33)

0.96 (0.94–0.98)

0.15

0.05

0.80 (0.77–0.83)

0.69 (0.66–0.73)

0.83 (0.81–0.86)

0.21

0.2

0.70 (0.66–0.73)

0.68 (0.64–0.72)

0.71 (0.67–0.74)

0.15

0.2

0.01

0.79 (0.73–0.85)

0.20 (0.16–0.25)

0.98 (0.96–1.00)

0.17

0.05

0.75 (0.72–0.79)

0.64 (0.60–0.69)

0.83 (0.80–0.86)

0.19

0.2

0.68 (0.64–0.72)

0.65 (0.61–0.70)

0.68 (0.64–0.72)

0.14

0.8

0.001

0.01

0.93 (0.90–0.95)

0.50 (0.43–0.55)

0.99 (0.98–1.00)

0.42

0.05

0.92 (0.90–0.93)

0.82 (0.79–0.85)

0.94 (0.93–0.95)

0.46

0.2

0.91 (0.90–0.92)

0.88 (0.87–0.90)

0.87 (0.85–0.89)

0.39

0.01

0.01

0.91 (0.88–0.93)

0.50 (0.46–0.55)

0.98 (0.97–0.99)

0.31

0.05

0.91 (0.90–0.93)

0.83 (0.80–0.85)

0.93 (0.91–0.94)

0.41

0.2

0.89 (0.87–0.90)

0.85 (0.82–0.87)

0.86 (0.84–0.88)

0.33

0.1

0.01

0.84 (0.79–0.89)

0.36 (0.31–0.42)

0.98 (0.96–0.99)

0.21

0.05

0.86 (0.83–0.88)

0.75 (0.72–0.78)

0.89 (0.86–0.91)

0.28

0.2

0.82 (0.79–0.84)

0.78 (0.75–0.81)

0.80 (0.77–0.83)

0.22

0.2

0.01

0.75 (0.69–0.81)

0.35 (0.30–0.40)

0.94 (0.91–0.97)

0.14

0.05

0.84 (0.82–0.87)

0.72 (0.69–0.76)

0.88 (0.86–0.90)

0.26

0.2

0.78 (0.75–0.81)

0.73 (0.70–0.77)

0.78 (0.75–0.81)

0.20

  1. Polygenicity proportion of causal variants of all simulated variants, AUC area under the ROC curve, PPV positive predictive value, NPV negative predictive value, Coverage proportion of samples predicted as case or control, 95% CI 95% confidence interval.