Another interesting possibility to consider is the impact of larger HapMap reference panel on imputation or, similarly, the utility of using extra genotype data on a subset of individuals in a study to aid imputation in the remaining individuals in the study. To evaluate these possibilities, we generated a reference panel with varying numbers of Finnish individuals (between 30 and 500, see Table V) and used these reference panels to impute genotypes for 521 SNPs in an independent set of 500 individuals from the FUSION study of type II diabetes. Imputation accuracy and genomic coverage increase noticeably with the larger reference panels, with overall discrepancy rates between typed and untyped alleles as low as 0.40% when a reference panel of 500 unrelated individuals is available. One of the reasons for this increase in accuracy is that the length of haplotypes shared between individuals in the reference panel and those in the study sample increases gradually as the size of the reference panel increases. For example, mosaic fragments used to reconstitute the FUSION samples using the individuals in the 500-sample reference
