We used genotype data from the Wellcome Trust Case Control Consortium 2 (WTCCC2)10 on members of the 1958 British Birth Cohort, which is comprised of controls sampled from the United Kingdom. These individuals were genotyped on Affymetrix 6.0 and Illumina 1.2 M SNP arrays. The WTCCC2 merged genotypes across platforms and applied standard QC filters, which resulted in 2,490 individuals and 71,190 SNPs on chromosome 10. For our imputation experiments we masked the SNPs not found on the Affymetrix 500k array, imputed the masked SNPs, and compared the imputed dosages against the original array genotypes.
