used to augment study controls to increase sample size and boost statistical power (Ho and Lange 2010). These study designs extend the scientific and societal benefits from the financial and time investments made by the original studies’ funding agencies and investigators, providing a cost-effective strategy to obtain the large number of control subjects needed for GWAS analyses. This strategy may be particularly beneficial for ancestry groups with few available samples (e.g., African Americans) (Hartz et al. 2011). Thus, continued examination and development of methods to produce valid SNP imputation across historic and new genotyping arrays is well worth the investment. Use of the intersecting SNP strategy described in this study appears to be a cost-effective and valid approach to cross array imputation, avoiding previously observed biases and generating reasonable imputation quality across arrays with 30 % or more overlap in genotyped SNPs.
