The UK Biobank genetic data contains genotypes for 488,377 participants. These were assayed using two very similar genotyping arrays. A subset of 49,950 participants involved in the UK Biobank Lung Exome Variant Evaluation (UK BiLEVE) study were genotyped at 807,411 markers using the Applied Biosystems UK BiLEVE Axiom Array by Affymetrix (now part of Thermo Fisher Scientific), which is described elsewhere6. Following this, 438,427 participants were genotyped using the closely related Applied Biosystems UK Biobank Axiom Array (825,927 markers) that shares 95% of marker content with the UK BiLEVE Axiom Array. The marker content of the UK Biobank Axiom array was chosen to capture genome-wide genetic variation (single nucleotide polymorphism (SNPs) and short insertions and deletions (indels)), and is summarized in Fig. 1. Many markers were included because of known associations with, or possible roles in, disease. The array also includes coding variants across a range of minor allele frequencies (MAFs), including rare markers (<1% MAF); and markers that provide good genome-wide coverage for imputation in European populations in the common (>5%) and low frequency (1–5%) MAF ranges. Further details of the array design are in the UK Biobank Axiom Array Content Summary2.
