Table 1 CardioBoost outperforms existing genome-wide tools for the classification of holdout test variants.

From: Disease-specific variant pathogenicity prediction significantly improves variant interpretation in inherited cardiac conditions

%

Cardiomyopathies

Arrhythmias

CardioBoost

M-CAP

REVEL

CardioBoost

M-CAP

REVEL

Overall accuracy

63.3a

28.4

17.4

81.2a

30.5

37

Proportion of variants classified with high confidence

70.2a

33.9

22

88.3a

33.8

40.3

Accuracy of high-confidence classifications

90.2

83.8

79.2

91.9

90.4

91.9

Proportion of variants with indeterminate classification

29.8a

66.1

78

11.7a

66.2

59.7

 TPR

69.5a

41.5

28

83.3a

48.8

65.5

 PPV

86.3

81.7

76.7

90.9

91.1

91.7

 TNR

56a

13

5

78.6a

8.6

2.9

 NPV

96.6

92.9

100

93.2

85.7

100

  1. The performance of each tool is reported using the clinically relevant variant classification thresholds: high-confidence disease-causing (Pr ≥ 0.9), high-confidence benign (Pr ≤ 0.1), and indeterminate. For each predictive performance measure (see Supplementary Methods for details) the best algorithm is highlighted in bold. Permutation tests were performed to evaluate whether the performance of CardioBoost was significantly different from the best value obtained by M-CAP or REVEL.
  2. NPV negative predictive value, PPV positive predictive value, TNR true negative rate, TPR true positive rate.
  3. aP value ≤ 0.001.