PedGenie: meta genetic association testing in mixed family and case-control designs

BMC Bioinformatics

Table 1 Simulated study characteristics, null scenario.

Study	Description	Pop. MAF	Sample size (N)			Study cases				Study controls
			Total	Cases	Ctrls.	MAF	AA	Aa	aa	MAF	AA	Aa	aa
Independent design meta-analytic datasets
1.1	Case-control	0.05	2000	1000	1000	0.06	892	105	3	0.05	898	100	2
1.2	Case-control	0.10	1000	500	500	0.10	404	91	5	0.10	409	86	5
1.3	Case-control	0.20	500	250	250	0.19	162	79	9	0.21	156	84	10
Mixed design meta-analytic datasets
2.1	Case-control	0.05	2000	1000	1000	0.06	892	105	3	0.05	898	100	2
2.2	Nuclear families and independents¹	0.10	1800	675	1125	0.10	546	120	9	0.10	915	196	14
2.3	Pedigrees and independents²	0.20	4550	501	4049	0.19	333	147	21	0.20	2584	1279	186

¹400 affected sibs in affected sib-pairs (ASPs), 200 affected sibs in discordant sib-pairs (DSPs), and 75 family cases; 200 unaffected sibs in DSPs, 725 family, and 200 independent controls.
²501 family cases and 3,549 family controls in 90 four-generation pedigrees (founders and first generation ungenotyped), 500 independent controls.

ISSN: 1471-2105