SNPs genotyped in each study as proxies for SNPs genotyped in the other studies [Carlson et al., 2004; de Bakker et al., 2005; Lin et al., 2004; Nicolae, 2006; Zaitlen et al., 2007], meta-analyses of GWAS conducted in this manner would be cumbersome because of the limited overlap between the different commercial panels and because different choices of proxies for a particular SNP might lead to somewhat different conclusions.
