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 (
link) 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 1
22 (
link) and
UK10K Project
23,24 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.
Using data from previously published studies of whole-genome gene expression and genome-wide genotyping,
25–29 we assessed whether variants at associated loci (identified as described in the Statistical analysis) regulate levels of mRNA. These expression quantitative trait loci (eQTL) studies included non-tumour lung tissue, blood, and, for variants associated with smoking behaviour, brain. For genes close to peaks of novel signals or genes implicated through eQTL, we assessed differential expression in the lungs of individuals with and without COPD and differential expression in the pseudoglandular and canalicular stages of development of the fetal lung.
30,31 Additionally, we generated RNA sequencing data to discover novel transcripts of these genes in human bronchial epithelial cells. We tested all genome-wide meta-analysis p values for enrichment in biological pathways defined in publicly available databases. All functional analyses are described in detail in the
appendix (pp 21–23).
Wain L.V., Shrine N., Miller S., Jackson V.E., Ntalla I., Artigas M.S., Billington C.K., Kheirallah A.K., Allen R., Cook J.P., Probert K., Obeidat M., Bossé Y., Hao K., Postma D.S., Paré P.D., Ramasamy A., Mägi R., Mihailov E., Reinmaa E., Melén E., O'Connell J., Frangou E., Delaneau O., Freeman C., Petkova D., McCarthy M., Sayers I., Deloukas P., Hubbard R., Pavord I., Hansell A.L., Thomson N.C., Zeggini E., Morris A.P., Marchini J., Strachan D.P., Tobin M.D, & Hall I.P. (2015). Novel insights into the genetics of smoking behaviour, lung function, and chronic obstructive pulmonary disease (UK BiLEVE): a genetic association study in UK Biobank. The Lancet. Respiratory Medicine, 3(10), 769-781.