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

BMC Bioinformatics

Table 2 Simulated study characteristics, alternate 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	0.07	865	130	5	0.05	906	92	2
1.2	Case-control	0.10	1000	500	500	0.13	375	116	9	0.09	413	83	4
1.3	Case-control	0.20	500	250	250	0.26	136	96	18	0.19	163	80	7
Mixed design meta-analytic datasets
2.1	Case-control	0.05	2000	1000	1000	0.07	865	130	5	0.05	906	92	2
2.2	Nuclear families and independents¹	0.10	1800	694	1106	0.16	496	180	18	0.12	853	242	11
2.3	Pedigrees and independents²	0.20	4190	503	3687	0.23	294	184	25	0.19	2386	1184	117

¹400 affected sibs in ASPs, 200 affected sibs in DSPs, and 94 family cases; 200 unaffected sibs in DSPs, 706 family, and 200 independent controls.
²503 family cases and 3,187 family controls in 83 four-generation pedigrees (founders and first generation ungenotyped), 500 independent controls.

ISSN: 1471-2105