An alternative to using the HapMap samples as a reference is to genotype a subset of study samples for additional markers of interest and then use these as templates for genotype imputation in the remaining samples. This approach was used by Chambers et al (14) to combine data across three different platforms in a recent study of the genetics of obesity focused on individuals of South Asian ancestry. Compared to approaches that use the HapMap as a reference, this strategy can greatly reduce imputation error (14).
