UK Biobank Exome Sequencing and SNP Genotyping

Next generation exome sequencing data were available on 49 960 participants, of whom 49 908 also had SNP chip data that had passed quality control. SNP chip data were generated centrally by the UK Biobank, and the exome sequencing data were generated externally by Regeneron and returned to the UK Biobank resource as part of an external access application request.20 (link) A subset of 4037 participants were previously genotyped using the Applied Biosystems UK BiLEVE Axiom Array by Affymetrix (807 411 genetic markers), and the other 45 871 participants were previously genotyped using the Applied Biosystems UK Biobank Axiom Array (825 927 genetic markers) that shares 95% of its marker content with the BiLEVE.10 (link) Participants were genotyped in 106 batches of around 5000 samples. We included samples that passed central UK Biobank quality control on either of the UK Biobank SNP chips and used standard quality metrics to exclude problematic SNPs (missingness rate <5% and Hardy Weinberg P<1×10⁻⁶).11 (link) We used the UCSC genome browser liftover tool to convert SNP chip variant positions that were reported in human genome build 37 to 38 coordinates for direct comparison with sequencing data.