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Table 2 Stratified sensitivities by effect sizes and number of causal SNPs under simulation

From: Relative performance of gene- and pathway-level methods as secondary analyses for genome-wide association studies

Group

Method

Sensitivity (OR* = 2)

Sensitivity (OR* = 1.2)

Sensitivity (1 SNP)

Sensitivity (2 SNPs)

Sensitivity (5 SNPs)

Classical

Fisher

66%

17%

50%

64%

60%

Sidak

18%

33%

12%

18%

20%

Simes

50%

17%

50%

50%

45%

FDR

27%

17%

25%

27%

25%

Updated Classical

TPM

68%

20%

57%

63%

65%

GATES

25%

17%

12%

18%

35%

GATES [Weighted]

27%

17%

25%

18%

30%

HYST

25%

17%

12%

18%

40%

Weighted GATES/HYST

25%

17%

12%

18%

35%

Novel

VEGAS

23%

17%

0%

27%

25%

VEGAS [10%]

32%

17%

0%

32%

40%

  1. Sensitivity and specificity calculated using subset of 49 true positive and 50 true negative genes. False positive and false negative percentages calculated using entire dataset of ~17,000 genes.
  2. *OR = Odds Ratio.