Table 2

Overall false- and true-positive rates for the four rare variant methods (significance level 5%)

Rare variant method

False-positive rate (%)

True-positive rate (%)


Only SNPs with MAF < 5%

All SNPs

Only nonsynonymous SNPs

Only SNPs with MAF < 5%

All SNPs

Only nonsynonymous SNPs


WS

9.7

10.8

9.3

15.8

18.9

14.6

CMAT

6.9

9.2

7.8

12.3

12.8

11.6

CMC

8.9

11.2

10.1

10.6

14.3

13.9

PR

6.3

8.9

7.6

12.4

13.2

10.8


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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