Table 2.

Descriptive summary of three study designs

Model	α	Genetic model	Design	p (true minor allele freq.)	p̂case	Avg. (SD) number of cases	p̂control (n = 500)	Avg. proportion of cases from linked subset	$T_{\mathit{\text{design}}}^2$	Rdesign	True marginal OR(G)	ÔR(G) at SNP252
												Avg.	SD
1	0.2	dom	A	0.1	0.173	1,000 (–)	0.087	0.2	48.99	1	10.84	1.85	0.22
			B	0.1	0.181	307 (14.6)	0.087	0.213	27.54	0.59	10.84	1.90	0.29
			C	0.1	0.268	248 (171)	0.087	0.388	68.98	3.98	10.84	1.89	0.28
	0.2	rec	A	0.35	0.453	1,000	0.331	0.2	43.1	1	13.16	1.52	0.12
			B	0.35	0.485	315 (14.4)	0.331	0.239	38.38	1.46	13.16	1.56	0.18
			C	0.35	0.575	297 (196)	0.331	0.349	94.08	8.97	13.16	1.69	0.15
	0.5	dom	A	0.05	0.168	1,000 (–)	0.044	0.5	137.34	1	7.52	2.38	0.45
			B	0.05	0.186	308 (13.7)	0.044	0.514	70.05	0.48	7.52	2.55	0.58
			C	0.05	0.381	331 (204)	0.044	0.713	285.12	7.78	7.52	3.79	0.85
	0.5	rec	A	0.35	0.534	1,000 (–)	0.340	0.5	107.89	1	8.93	1.45	0.11
			B	0.35	0.586	323 (14.8)	0.340	0.538	100.87	1.59	8.93	1.54	0.15
			C	0.35	0.804	413 (211)	0.340	0.705	518.56	37.95	8.93	1.85	0.19
2	0.2	dom	A	0.1	0.172	1,000 (–)	0.097	0.2	35.42	1	3.37	1.30	0.20
			B	0.1	0.182	307 (14.6)	0.097	0.215	21.89	0.71	3.37	1.36	0.24
			C	0.1	0.249	297 (196)	0.097	0.329	57.41	4.94	3.37	1.70	0.39
	0.2	rec	A	0.35	0.455	1,000 (–)	0.346	0.2	33.92	1	4.44	1.16	0.09
			B	0.35	0.486	315 (14.4)	0.346	0.238	31.47	1.58	4.44	1.23	0.12
			C	0.35	0.545	297 (196)	0.346	0.330	61.52	6.19	4.44	1.41	0.26
	0.5	dom	A	0.05	0.162	1,000 (–)	0.047	0.5	117.38	1	3.32	1.91	0.35
			B	0.05	0.183	308 (13.7)	0.047	0.509	64.33	0.56	3.32	2.12	0.45
			C	0.05	0.231	331 (204)	0.047	0.593	108.12	1.53	3.32	2.59	0.66
	0.5	rec	A	0.35	0.541	1,000 (–)	0.344	0.5	110.94	1	4.03	1.31	0.10
			B	0.35	0.594	323 (14.8)	0.344	0.540	104.34	1.61	4.03	1.41	0.15
			C	0.35	0.630	413 (210)	0.344	0.618	161.06	3.46	4.03	1.53	0.17
3	0.2	dom	A	0.1	0.173	1,000 (–)	0.087	0.2	48.99	1	2.90	1.32	0.18
			B	0.1	0.183	307 (14.9)	0.087	0.219	28.54	0.63	2.90	1.36	0.23
			C	0.1	0.420	208 (81)	0.087	0.822	166.75	24.54	2.90	2.65	0.57
	0.2	rec	A	0.35	0.455	1,000 (–)	0.332	0.2	43.76	1	3.36	1.18	0.09
			B	0.35	0.485	314 (14.3)	0.332	0.239	37.79	1.37	3.36	1.24	0.13
			C	0.35	0.823	210 (65)	0.332	0.916	423.98	198.37	3.36	1.94	0.28
	0.5	dom	A	0.05	0.166	1,000 (–)	0.043	0.5	137.07	1	3.10	1.95	0.37
			B	0.05	0.183	309 (13.9)	0.043	0.512	69.24	0.47	3.10	2.12	0.47
			C	0.05	0.270	456 (145)	0.043	0.912	200.29	3.35	3.10	2.88	0.60
	0.5	rec	A	0.35	0.538	1,000 (–)	0.338	0.5	114.93	1	3.50	1.32	0.11
			B	0.35	0.590	322 (14.2)	0.338	0.543	105.95	1.55	3.50	1.43	0.15
			C	0.35	0.707	487 (102)	0.338	0.948	311.98	11.2	3.50	1.65	0.17

Average minor allele frequency at QTL or DSL in cases and controls, average number of cases, and average proportion of cases from linked subset of families are shown for each simulation model and study design (for r² = 0.1). $T_{\mathit{\text{design}}}^2$ and R_design are defined in the Methods section. The true marginal OR(G) was calculated from the simulation parameters (see appendix for details), and the estimated ÔR(G) at SNP 252 (average and SD) was calculated from the simulated datasets. All averages were calculated across replicates that met the linkage thresholds for MERLIN (Designs A and B) or OSA (Design C), as explained in the text.