slightly from ours; however, we believe that the most important difference was the nested structure of their design – that is, that their central control group had SNPs from both Affy and Illumina chips, rather than Illumina alone. A comparison of their results and ours suggests that if a central control group is going to be reused for different diseases, it may be wise to invest in genotyping the central control group on multiple platforms. A similar conclusion is offered by Marchini and Howie (2010).
