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

BMC Proceedings

Table 4 Type I error and power at α = 5% by gene in family data set

Gene	N	N (V) with MAF < 5%	N (V) with MAF < 1%	SM^a	T_maf = 0.01		T_maf = 0.05		WS	CMC1
					CA	CP	CA	CP
Noncausal genes: type I error
PTGFR	7	4 (0)	7 (0)	0.030	0.095	0.065	0.015	0.010	0.070	0.030
IFI44	9	7 (0)	8 (0)	0.060	0.030	0.025	0.030	0.040	0.010	0.175
FAM73A	3	3 (0)	3 (0)	0.025	0.020	0.020	0.015	0.020	0.035	n/a
MAPT	19	8 (0)	14 (0)	0.210	0.145	0.180	0.035	0.010	0.155	0.015
CTSS	3	2 (0)	2 (0)	0.020	0.015	0.015	0.015	0.015	0.020	n/a
FOXI1	5	3 (0)	3 (0)	0.020	0.020	0.055	0.055	0.055	0.045	0.000
LY75	49	30 (0)	39 (0)	0.055	0.070	0.045	0.030	0.035	0.120	0.035
Causal genes: power
ARNT	7	6 (2)	4 (1)	0.04	0.04	0.03	0.01	0.01	0.12	0.03
ELAVL4	8	6 (1)	5 (1)	0.13	0.07	0.07	0.10	0.10	0.04	0.07
FLT1	16	13 (4)	8 (2)	0.95	0.02	0.02	0.57	0.82	0.44	0.33
FLT4	3	3 (0)	2 (0)	0.04	0.16	0.16	0.17	0.17	0.12	0.10
HIF1A	1	1 (1)	0 (0)	0.01	n/a	n/a	0.05	n/a	0.05	n/a
HIF3A	12	8 (1)	6 (1)	0.10	0.01	0.01	0.04	0.05	0.13	0.03
KDR	5	4 (4)	3 (3)	0.61	0.51	0.51	0.89	0.89	0.91	0.82
VEGFA	4	4 (1)	3 (1)	1	1	1	1	1	0.82	1
VEGFC	1	1 (1)	1 (1)	1	n/a	n/a	n/a	n/a	n/a	n/a

ISSN: 1753-6561