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

BMC Proceedings

Table 3 Power 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
ARNT	0.86	0.04	0.04	0.79	0.83	0.53	0.76	0.93	0.96	0.94
ELAVL4	0.31	0.05	0.05	0.05	0.05	0.00	0.06	0.07	0.07	0.41
FLT1	0.99	0.85	0.91	1.00	1.00	1.00	1.00	1.00	1.00	1.00
FLT4	0.33	0.41	0.38	0.65	0.62	0.78	0.76	0.50	0.47	n/a
HIF1A	0.42	0.07	0.07	0.62	0.59	0.45	0.51	0.62	0.62	n/a
HIF3A	0.02	0.03	0.02	0.07	0.07	0.06	0.04	0.20	0.17	0.10
KDR	0.96	0.97	0.99	1.00	1.00	1.00	1.00	0.99	0.99	1.00
VEGFA	0.26	0.13	0.13	0.41	0.44	0.54	0.45	0.31	0.31	n/a
VEGFC	0.58	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a
Q1 adjusted for the top five principal components
ARNT	0.44	0.05	0.05	0.49	0.05	0.37	0.44	0.56	0.67	0.60
ELAVL4	0.07	0.07	0.07	0.07	0.07	0.05	0.12	0.06	0.06	0.01
FLT1	1.00	0.67	0.80	0.98	1.00	1.00	1.00	0.99	1.00	1.00
FLT4	0.09	0.03	0.02	0.04	0.03	0.01	0.02	0.04	0.06	n/a
HIF1A	0.13	0.08	0.08	0.00	0.01	0.01	0.01	0.19	0.19	n/a
HIF3A	0.03	0.05	0.03	0.01	0.00	0.00	0.00	0.03	0.04	0.03
KDR	0.74	0.63	0.74	0.84	0.85	0.99	0.93	0.72	0.69	0.78
VEGFA	0.25	0.13	0.13	0.04	0.06	0.19	0.32	0.08	0.10	n/a
VEGFC	0.56	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a	n/a

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

ISSN: 1753-6561