We undertook genome-wide genotyping of variants using a new custom Affymetrix Axiom array (UK BiLEVE array; Santa Clara, CA, USA; appendix pp 5–8) that was designed to (1) measure rare coding variation; (2) provide a framework for optimum imputation of non-genotyped variants that are common (MAF >5%) or of low frequency (MAF 1–5%) in the European population, when used in conjunction with a large imputation reference panel of individuals with whole-genome sequence data;21 and (3) optimise coverage of genes and genomic regions with established or putative roles in lung health and disease to enable fine mapping. After thorough sample and variant quality control (appendix pp 8–15), we imputed non-genotyped variants using a combined 1000 Genomes Project Phase 122 and UK10K Project23,24 reference panel (appendix pp 15–16). The data were used to finalise the design of the UK Biobank array, which is being used for genome-wide genotyping and imputation of the remaining UK Biobank participants.
