Table 2.

Comparison of Different Analysis Strategies under the Null Hypothesis, with 5% Missing Data

	Average LOD			Information Content			Significance Threshold for α=.05a
Analysis Strategy	Ignore LD	Model LD	Independent SNPs	Ignore LD	Model LD	Independent SNPs	Ignore LD	Model LD	Independent SNPs
No parents genotyped:
2 sibs per family	1.539	−.004	−.004	.397	.378	.230	11.81	1.29	1.23
3 sibs per family	2.699	.003	.002	.531	.521	.336	18.11	1.34	1.23
4 sibs per family	2.380	−.006	−.007	.631	.627	.426	15.54	1.26	1.20
One parent genotyped:
2 sibs per family	.549	−.003	−.004	.683	.680	.432	5.40	1.40	1.29
3 sibs per family	.682	−.004	−.007	.769	.769	.534	6.18	1.31	1.23
4 sibs per family	.508	−.001	−.001	.820	.821	.603	4.62	1.38	1.25
Two parents genotyped:
2 sibs per family	.032	−.001	−.001	.781	.784	.561	1.54	1.43	1.32
3 sibs per family	.027	−.002	−.004	.823	.825	.619	1.52	1.41	1.35
4 sibs per family	.024	.003	.003	.849	.850	.659	1.49	1.40	1.32

^aIn simulated ∼100-cM chromosome.