Inference of disease associations with unmeasured genetic variants by combining results from genome-wide association studies with linkage disequilibrium patterns in a reference data set

Table 1 Effect of different choices of tagSNP inclusion criteria on estimation of Φ

	Minimum r²				Maximum r²
	0	0.2	0.4	0.6	0.1	0.3	0.5	0.7
Pooled Φ	0.453	0.4046	0.4065	0.4253	0.3768	0.5104	0.4569	0.4530
SE of pooled Φ	0.0258	0.0256	0.0256	0.0256	0.0352	0.0292	0.0263	0.0257
Number of tagSNPs used in estimate	156	21	12	3	102	135	153	156

Different combinations of tagSNPs from the NARAC case-control data set, selected by inclusion based on r² between the tagSNPs and the DRB1*04 allele, give slightly different effect estimates (Φ). Also shown is the standard error of Φ under the null hypothesis, derived empirically from 1000 random permutations of the B58C data set.

ISSN: 1753-6561