One new data configuration, which we call Scenario B and explore in detail in the current study, is presented in Figure 2; we will address other next-generation reference panels in the Discussion. In Scenario B, there are different amounts of genotype data in different cohorts of a study. For example, the Wellcome Trust Case Control Consortium (WTCCC) is currently performing an association study in which 6,000 controls will be genotyped on both the Affymetrix 6.0 and Illumina 1 M SNP chips, whereas disease cohorts will be genotyped only on either the Affymetrix 6.0 chip or the Illumina 670 k chip. In other words, a large set of controls will be genotyped at a subset of HapMap SNPs, and each case cohort will be genotyped at a subset of the SNPs typed in the controls. Published studies have already employed this design [14], and it may become more prevalent in the future as common sets of population controls become more widely available.
