Comparative study of statistical methods for detecting association with rare variants in exome-resequencing data

BMC Proceedings

Table 2 Type I error rates at α = 5% by gene in the unrelated individuals data set

Gene	SM^a	T_maf = 0.01		T_maf = 0.05		WS	VT	CMC1	CMC2	CMC3
		CA	CP	CA	CP
Unadjusted Q1
CTSS	0.020	0.005	0.005	0.030	0.040	0.055	0.020	0.020	0.020	0.030
FAM73A	0.020	0.035	0.035	n/a	n/a	0.075	0.055	n/a	n/a	n/a
FOXI1	0.150	0.040	0.030	0.040	0.030	0.000	0.000	n/a	n/a	0.110
PTGFR	0.040	0.020	0.025	0.025	0.025	0.010	0.080	0.035	0.040	n/a
IFI44	0.350	0.055	0.050	0.110	0.140	0.040	0.120	0.305	0.305	0.220
MAPT	0.175	0.100	0.200	0.610	0.350	0.555	0.390	0.130	0.110	0.115
LY75	0.075	0.010	0.005	0.015	0.030	0.020	0.010	0.065	0.075	0.155
Q1 adjusted for the top five principal components
CTSS	0.015	0.040	0.040	0.040	0.040	0.125	0.060	0.025	0.030	0.045
FAM73A	0.025	0.005	0.005	n/a	n/a	0.020	0.020	n/a	n/a	n/a
FOXI1	0.040	0.020	0.030	0.020	0.030	0.000	0.000	n/a	n/a	0.035
PTGFR	0.015	0.065	0.025	0.010	0.015	0.125	0.060	0.035	0.030	n/a
IFI44	0.075	0.030	0.025	0.010	0.015	0.010	0.015	0.020	0.020	0.000
MAPT	0.055	0.010	0.015	0.025	0.040	0.010	0.005	0.010	0.050	0.215
LY75	0.055	0.005	0.010	0.010	0.010	0.060	0.030	0.015	0.025	0.015

Estimates outside the 95% confidence interval are underlined. n/a, not applicable.
^a Bonferroni-corrected P-value.

ISSN: 1753-6561