BMC Proceedings

Table 1 Estimated type I error rates at nominal level 0.05, 1000 replicate simulation data sets

From: Genome-wide association tests by two-stage approaches with unified analysis of families and unrelated individuals

			Two children in each family^b				One child in each family^b
Sample size	Minor allele frequency	α ^a	PDT	T _pc	T _cc	T _cb	PDT	T _pc	T _cc	T _cb
100 families, 120 controls	0.1	0.05	0.014	0.032	0.043	0.042	0.031	0.033	0.044	0.043
		0.1		0.023	0.028	0.032		0.029	0.041	0.029
		0.2		0.025	0.027	0.027		0.031	0.031	0.026
	0.3	0.05	0.024	0.042	0.049	0.047	0.036	0.05	0.045	0.053
		0.1		0.04	0.043	0.035		0.051	0.047	0.046
		0.2		0.046	0.038	0.037		0.054	0.047	0.053
500 families, 600 controls	0.1	0.05	0.048	0.051	0.051	0.059	0.053	0.052	0.054	0.051
		0.1		0.04	0.052	0.042		0.052	0.041	0.045
		0.2		0.042	0.046	0.044		0.04	0.047	0.05
	0.3	0.05	0.059	0.053	0.047	0.045	0.042	0.046	0.04	0.042
		0.1		0.054	0.042	0.046		0.048	0.034	0.044
		0.2		0.053	0.034	0.048		0.047	0.043	0.041

^aα, the cut-off p-value of the test in the first stage
^bPDT, pedigree disequilibrium test; T_pc, test comparing all parents to controls; T_cc, test comparing affected and unaffected parents; T_cb, combined T_pcand T_cc

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