Table 1

Overall ability of the four rare variant methods to identify genes as significantly associated with the phenotype

Method

Nominal α = 0.05

Nominal α = 0.005


Total number of significant associations

Number of significant associations that are actually causal

True discoveries (%)

Total number of significant associations

Number of significant associations that are actually causal

True discoveries (%)


Only SNPs with MAF < 5%

WS

281.0

5.69

2.03

52.5

1.56

2.97

CMAT

201.4

4.42

2.19

38.4

1.31

3.44

CMC

256.5

3.80

1.48

38.2

0.92

2.41

PR

184.6

4.46

2.41

27.9

1.17

4.20

All SNPs

WS

348.7

6.81

1.95

76.1

2.05

2.69

CMAT

294.9

4.63

1.57

63.8

1.46

2.28

CMC

361.1

5.16

1.43

64.6

1.23

1.90

PR

285.6

4.74

1.66

53.7

1.39

2.59

Nonsynonymous SNPs only

WS

206.1

5.25

2.54

42.3

1.78

4.20

CMAT

173.3

4.19

2.42

35.7

1.44

4.03

CMC

223.3

4.99

2.23

38.5

1.33

3.46

PR

168.7

3.88

2.30

29.4

1.38

4.69


All values are averaged over 200 replicates. WS, weighted sum; CMAT, cumulative minor allele test; CMC, combined multivariate and collapsing; PR, proportion regression.

Luedtke et al. BMC Proceedings 2011 5(Suppl 9):S119   doi:10.1186/1753-6561-5-S9-S119

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