Another strategy to save funds, which can be spent instead on choosing a greater-coverage genotyping panel or preferably genotyping more cases, is to use publicly available genotyping data for common controls from another study such as the WTCCC project (provided that they have been sampled from the same underlying population as cases and that population structure is investigated and adjusted for at the analysis stage 2). Publicly available controls, however, are likely to have been genotyped on different panels, and if so, imputation would need to be performed to allow combined analyses.
