Combining effects from rare and common genetic variants in an exome-wide association study of sequence data

BMC Proceedings

Table 1 Comparison of power and type I error rate of single tests and combined tests

Method	Group 1		Group 2
	Power to detect the four causal genes	Type I error rate for α = 5%	Power to detect the five causal genes	Type I error rate for α = 5%
Rare variant tests
FT_1%	0	0.053	0	0.051
FT_5%	0	0.048	0	0.054
WE	0	0.047	0	0.051
VT	0	0.046	0	0.046
Common variant tests
CV_pmin,1%	–	–	0.200	0.052
CV_pmin,5%	–	–	0.200	0.049
CV_lasso,1%	–	–	0.094	0.056
CV_lasso,5%	–	–	0.158	0.059
Combined tests
Comb_(pmin+FT),1%	–	–	0.230	0.057
Comb_(pmin+FT),5%	–	–	0.202	0.058
Comb_{(lasso+FT),1%}	–	–	0.182	0.060
Comb_{(lasso+FT),5%}	–	–	0.196	0.054

Type I error rate and power were computed over 100 replicates after genomic control adjustment. Group 1 includes genes that have only rare variants; these genes have been analyzed using rare variant approaches only. Group 2 includes genes that have both rare and common variants. FT, fixed threshold test; WE, weighted test; VT, variable threshold test; CV_pmin, common variants test using p-min; CV_lasso, common variants test using LASSO; Comb, combined test. Tests that depend on a threshold are indicated with the subscript T (1% or 5%).

ISSN: 1753-6561