Table 1.

Overview of Study Design

Disease	Type	Study	Design	Ncase/Ncontrol	NSNP	GWAS Selection Criteria	Correction Cutoff
Lung Cancer	Discovery	UTMD	One Stage	1,154/1,137	315,450	Top ranked 101	P1 = 4.5 × 10−5
	Replication	Texas&UK		2,724/3,694	10
Colorectal Cancer	Meta-analysis	London&Edinburgh	One Stage	4878/4914	38,710	P1 < 5.0 × 10−5	P1 = 5.0 × 10−5
	Replication	4 cohorts		13,114/14,304	7
T1D	GWAS	WTCCC	One Stage	1,924/2,938	393,143	P1 < 10−5	P1 = 1.64 × 10−5
	Replication	Todd		4,000/5,000	11
Prostate Cancer	GWAS	Eeles	One Stage	1,854/1,894	541,129	P1 < 10−6	P1 = 10−6
	Replication	UK&Australia		3,268/3,366	11
Breast Cancer	GWAS	Easton	Two Stage	Stage I: 390/364	Stage I 205,586	Top ranked 5%1 (N=12,711)	P1 = 0.05
				Stage II: 3,990/3,916	Stage II 10,405	Top ranked and candidate gene2	P1combine = 2.3 × 10−3
	Replication	22 cohorts		21,860/22,578	30
	GWAS	CGEMS	One Stage	1,145/1,142	528,173	Top ranked 63	P3 = 1.5 × 10−5
	Replication	3 cohorts		1,776/2,072	8
T2D	Meta-analysis	Diagram	Two Stage	Stage I: 4,549/5,579	Stage I: 2,202,892	Top ranked 691	P1 = 3.1 × 10−5
				Stage II: 10,037/12,389	Stage II: 69	P1combine < 10−5	P1combine = 10−5
	Replication	10 cohorts		14,157/43,209	11

¹P-values are computed from 1 degree of freedom association trend tests;

²P-values are computed from 1 degree of freedom association tests, combining stages 1 and 2;

³P-values are either from 1 degree of freedom association tests or a score test with two degrees of freedom.