Table 1:

Empirical type I error rates of the Multi-SKAT tests from 5,000,000 simulated null datasets. The number of phenotypes were nine and the correlation structure among the phenotypes were similar to that of the amino acid phenotypes in the METSIM study data. The sample size was 5000.

	Level	Σ G	minPhen	Hom	Het	PhC	PC-Sel	minP	minPcom
	2.5 × 10−06	SKAT	2.4 × 10−06	2.6 × 10−06	2.6 × 10−06	2.8 × 10−06	2.6 × 10−06	3.4 × 10−06	2.8 × 10−06
		Burden	2.4 × 10−06	2.8 × 10−06	2.6 × 10−06	2.6 × 10−06	2.6 × 10−06	3.0 × 10−06
Independent samples (without kinship adjustment)	10−05	SKAT	9.6 × 10−06	9.6 × 10−06	9.8 × 10−06	9.8 × 10−06	9.8 × 10−06	9.4 × 10−06	1.2 × 10−05
		Burden	9.4 × 10−06	9.6 × 10−06	9.8 × 10−06	9.6 × 10−06	9.6 × 10−06	9.6 × 10−06
	10−04	SKAT	9.6 × 10−05	9.4 × 10−05	9.6 × 10−05	9.8 × 10−05	9.8 × 10−05	9.8 × 10−05	1.1 × 10−04
		Burden	9.8 × 10−05	9.6 × 10−05	9.4 × 10−05	9.7 × 10−05	9.6 × 10−05	9.7 × 10−05
	2.5 × 10−06	SKAT	2.2 × 10−06	2.4 × 10−06	2.4 × 10−06	2.8 × 10−06	2.6 × 10−06	3.0 × 10−06	2.6 × 10−06
		Burden	2.2 × 10−06	2.6 × 10−06	2.4 × 10−06	2.6 × 10−06	2.4 × 10−06	3.2 × 10−06
Related samples (with kinship adjustment)	10−05	SKAT	9.6 × 10−06	9.8 × 10−06	9.8 × 10−06	9.8 × 10−06	9.8 × 10−06	9.4 × 10−06	1.4 × 10−05
		Burden	9.7 × 10−06	9.6 × 10−06	9.4 × 10−06	9.4 × 10−06	9.4 × 10−06	9.4 × 10−06
	10−04	SKAT	9.4 × 10−05	9.6 × 10−05	9.7 × 10−05	9.8 × 10−05	9.4 × 10−05	9.8 × 10−05	1.2 × 10−04
		Burden	9.5 × 10−05	9.7 × 10−05	9.6 × 10−05	9.8 × 10−05	9.8 × 10−05	9.7 × 10−05