Researchers can make use of accumulating genetic resources to more economically and more powerfully understand the effects of genes on complex diseases. However, our findings add to a familiar refrain about GWA studies – that every step must be done with extreme care to avoid spurious results (McCarthy et al. 2008). More work needs to be done to determine the best approaches for combining cases and controls obtained from different sources. In any case-control study, cases and controls should be comparable, and recent studies have discussed how to control for differential population substructure when using publicly available controls (Zhuang et al. 2010; Luca et al. 2008). Our work emphasizes the need to control for technical errors caused by integrating data from different chips. Researchers attempting to use the sort of data we describe, in which cases and controls are genotyped on different chips, need to be aware of the high potential for false positives after imputation, and must guard against it or control for it. In particular, it is vitally important to technically validate any SNPs that appear significant before
