DNA was extracted from stored blood samples that had been collected from participants on their visit to a UK Biobank assessment centre. Genotyping was carried out by Affymetrix Research Services Laboratory in 106 sequential batches of approximately 4,700 samples (see Methods, Supplementary Table 12). Affymetrix applied a custom genotype calling pipeline and quality filtering optimized for biobank-scale genotyping experiments and the novel genotyping arrays, which contain markers that had not been previously typed using Affymetrix technology (see Methods). This resulted in a set of genotype calls for 489,212 samples at 812,428 unique markers (biallelic SNPs and indels) from both arrays, with which we conducted further quality control and analysis (Extended Data Table 2).
