On receipt of DNA samples, Affymetrix processed samples on the GeneTitan Multi-Channel (MC) Instrument in 96-well plates containing 94 UK Biobank samples and two control samples from the 1000 Genomes Project25. Genotypes were then called from the array intensity data, in units called ‘batches’ which consist of multiple plates. Across the entire cohort, there were 106 batches of 4,700 UK Biobank samples each (Supplementary Information, Supplementary Table 12). Following the earlier interim data release, Affymetrix developed a custom genotype calling pipeline that is optimized for biobank-scale genotyping experiments, which takes advantage of the multiple-batch design35. This pipeline was applied to all samples, including the 150,000 samples that were part of the interim data release. Consequently, some of the genotype calls for these samples may differ between the interim data release and this final data release (see below).
