A key ingredient for any imputation-based approach is to ensure that alleles are consistently labeled across studies. In our evaluation of FUSION and HGDP samples, using the HapMap as a reference, we were fortunate that a subset of the HapMap individuals were genotyped in each study for quality control. Contrasting the genotypes for these quality control samples with those generated by the HapMap Consortium made the usually laborious process of ensuring consistent allele labeling across labs much easier. We strongly recommend that all labs conducting GWAS genotype a small number of HapMap individuals for this purpose.
