Novel insights into the genetics of smoking behaviour, lung function, and chronic obstructive pulmonary disease (UK BiLEVE): a genetic association study in UK Biobank.
- Authors
- Wain, Louise V; Shrine, Nick; Miller, Suzanne; Jackson, Victoria E; Ntalla, Ioanna; Soler Artigas, MarΓa; Billington, Charlotte K; Kheirallah, Abdul Kader; Allen, Richard; Cook, James P; Probert, Kelly; Obeidat, Ma'en; BossΓ©, Yohan; Hao, Ke; Postma, Dirkje S; ParΓ©, Peter D; Ramasamy, Adaikalavan; UK Brain Expression Consortium (UKBEC); MΓ€gi, Reedik; Mihailov, Evelin; Reinmaa, Eva; MelΓ©n, Erik; O'Connell, Jared; Frangou, Eleni; Delaneau, Olivier; OxGSK Consortium; Freeman, Colin; Petkova, Desislava; McCarthy, Mark; Sayers, Ian; Deloukas, Panos; Hubbard, Richard; Pavord, Ian; Hansell, Anna L; Thomson, Neil C; Zeggini, Eleftheria; Morris, Andrew P; Marchini, Jonathan; Strachan, David P; Tobin, Martin D; Hall, Ian P
- Year
- 2015
- Journal
- The Lancet. Respiratory medicine
- PMID
- 26423011
- DOI
- 10.1016/S2213-2600(15)00283-0
- PMCID
- PMC4593935
BACKGROUND: Understanding the genetic basis of airflow obstruction and smoking behaviour is key to determining the pathophysiology of chronic obstructive pulmonary disease (COPD). We used UK Biobank data to study the genetic causes of smoking behaviour and lung health. METHODS: We sampled individuals of European ancestry from UK Biobank, from the middle and extremes of the forced expiratory volume in 1 s (FEV1) distribution among heavy smokers (mean 35 pack-years) and never smokers. We developed a custom array for UK Biobank to provide optimum genome-wide coverage of common and low-frequency variants, dense coverage of genomic regions already implicated in lung health and disease, and to assay rare coding variants relevant to the UK population. We investigated whether there were shared genetic causes between different phenotypes defined by extremes of FEV1. We also looked for novel variants associated with extremes of FEV1 and smoking behaviour and assessed regions of the genome that had already shown evidence for a role in lung health and disease. We set genome-wide significance at p<5βΓβ10(-8). FINDINGS: UK Biobank participants were recruited from March 15, 2006, to July 7, 2010. Sample selection for the UK BiLEVE study started on Nov 22, 2012, and was completed on Dec 20, 2012. We selected 50,008 unique samples: 10,002 individuals with low FEV1, 10,000 with average FEV1, and 5002 with high FEV1 from each of the heavy smoker and never smoker groups. We noted a substantial sharing of genetic causes of low FEV1 between heavy smokers and never smokers (p=2.29βΓβ10(-16)) and between individuals with and without doctor-diagnosed asthma (p=6.06βΓβ10(-11)). We discovered six novel genome-wide significant signals of association with extremes of FEV1, including signals at four novel loci (KANSL1, TSEN54, TET2, and RBM19/TBX5) and independent signals at two previously reported loci (NPNT and HLA-DQB1/HLA-DQA2). These variants also showed association with COPD, including in individuals with no history of smoking. The number of copies of a 150 kb region containing the 5' end of KANSL1, a gene that is important for epigenetic gene regulation, was associated with extremes of FEV1. We also discovered five new genome-wide significant signals for smoking behaviour, including a variant in NCAM1 (chromosome 11) and a variant on chromosome 2 (between TEX41 and PABPC1P2) that has a trans effect on expression of NCAM1 in brain tissue. INTERPRETATION: By sampling from the extremes of the lung function distribution in UK Biobank, we identified novel genetic causes of lung function and smoking behaviour. These results provide new insight into the specific mechanisms underlying airflow obstruction, COPD, and tobacco addiction, and show substantial shared genetic architecture underlying airflow obstruction across individuals, irrespective of smoking behaviour and other airway disease. FUNDING: Medical Research Council.
Sample selection strategyATS=American Thoracic Society. ERS=European Respiratory Society.34 FEV1=forced expiratory volume in 1 s. FVC= forced vital capacity. *See appendix (pp 3β5) for more details of sample selection.
Polygenic component of low forced expiratory volume in 1 s and shared polygenic component of different phenotypes defined by forced expiratory volume in 1 s, smoking, and doctor diagnosis of asthmaThe p value in the target population shown above the bars is for the p value threshold <0Β·5. The sample sizes differed between the comparisons; details of these and the assumptions used in the analyses are described in the appendix (pp 18β20). FEV1=forced expiratory volume in 1 s.
Manhattan plots for low versus high forced expiratory volume in 1 s in never smokers and heavy smokers and for heavy versus never smokersp values are from a Score test and have genomic control applied unless the MAC was less than 400 and Score test p<1Β·00 Γ 10β6, in which case p values are from a Firth test with no genomic control. Novel loci are underlined and novel signals at previously reported loci are shown in bold. The dashed red line shows the threshold for genome-wide significance (p<5 Γ 10β8). Variants with suggestive evidence of association (p<5 Γ 10β7) are coloured red. Quantileβquantile plots for these analyses are shown in the appendix (pp 113β116). FEV1=forced expiratory volume in 1 s. MAC=minor allele count.
| Name | Type |
|---|---|
| 1000 Genomes Project Phase 1 local | cohort |
| 15q25 locus | variant |
| airflow obstruction | phenotype |
| airway disease local | phenotype |
| ANKK1 | gene |
| asthma | phenotype |
| average FEV1 local | phenotype |
| Average percent predicted FEV1 local | phenotype |
| Bdnf | gene |
| brain | anatomy |
| brain tissue | anatomy |
| C20orf203 local | gene |
| C20orf203 SNP local | variant |
| case group | cohort |
| CCDC91 local | gene |
| chr12:114743533 local | variant |
| Chrna3 | gene |
| Chrna4 | gene |
| CHRNA5 | gene |
| chronic obstructive pulmonary disease | phenotype |
| Common genetic variants (MAF>5%) local | variant |
| Complex structural variation region local | variant |
| control group | cohort |
| controls | cohort |
| COPD | phenotype |
| COPD cases local | cohort |
| CRHR1 | gene |
| DBH | gene |
| discovery population local | cohort |
| DNA | drug |
| DNAH8 local | gene |
| Egfr | gene |
| Epigenetic mechanisms local | drug |
| European ancestry | cohort |
| European population | cohort |
| Extremes of FEV1 local | phenotype |
| fetal lung age local | phenotype |
| fetal lung development local | phenotype |
| FEV1 local | phenotype |
| FEV1 extremes local | phenotype |
| FEV1:FVC ratio local | phenotype |
| forced expiratory volume in 1 s (FEV1) local | phenotype |
| FVC local | phenotype |
| general population | cohort |
| General population cohorts local | cohort |
| genetic variants | cohort |
| genome-wide significant loci | cohort |
| Global Burden of Disease Study 2010 local | cohort |
| GOLD stage 2+ local | phenotype |
| GOLD Stage 2+ COPD local | phenotype |
| Grb2 | gene |
| GSTCD local | gene |
| heavy drinking | phenotype |
| height | phenotype |
| high FEV1 local | phenotype |
| High FEV1 strata local | phenotype |
| high-income countries | cohort |
| High percent predicted FEV1 local | phenotype |
| HLA-DQA2 | gene |
| HLA-DQB1 local | gene |
| HLA-DQB1/HLA-DQA2 common variant local | variant |
| independent discovery population local | cohort |
| independent target population local | cohort |
| Indoor air pollution local | drug |
| inhaled corticosteroid response local | phenotype |
| intergenic SNP near NCAM1 local | variant |
| INTS12 local | gene |
| inversion | variant |
| inversion 17q21.31 local | variant |
| KANSL1 | gene |
| KIAA0195 local | gene |
| large biobank local | cohort |
| LLGL2 local | gene |
| low FEV1 local | phenotype |
| Low FEV1 local | phenotype |
| Low percent predicted FEV1 local | phenotype |
| LPPR5 local | gene |
| LRRC37A4P local | gene |
| lung function | phenotype |
| lung health and disease local | phenotype |
| Mapt | gene |
| medulla | anatomy |
| NCAM1 | gene |
| never smokers | phenotype |
| Newly designed genotyping array local | drug |
| nicotine | drug |
| nicotine addiction | phenotype |
| nicotine dependence | phenotype |
| NOL4L local | gene |
| non-smoking individuals local | cohort |
| NPNT | gene |
| P3G Catalogue local | cohort |
| PABPC1P2 local | gene |
| participants without asthma local | cohort |
| percent predicted FEV1 local | phenotype |
| pulmonary fibrosis | phenotype |
| rare SNP on chromosome 12 local | variant |
| RBM19 local | gene |
| RBM19/TBX5 rare variant local | variant |
| reference panel | cohort |
| risk score local | drug |
| rs10193706 local | variant |
| rs10516526 local | variant |
| rs105165267 local | variant |
| rs12622738 local | variant |
| rs17843604 local | variant |
| rs2047409 local | variant |
| rs2532349 local | variant |
| rs34712979 local | variant |
| rs4466874 local | variant |
| rs6856422 local | variant |
| rs7218675 local | variant |
| rs7764819 local | variant |
| rs927334937 local | variant |
| rs9273359 local | variant |
| rs9274600 local | variant |
| rs953246 local | variant |
| RSRC1 local | gene |
| sentinel variant local | variant |
| SLMAP local | gene |
| smoking | phenotype |
| smoking behaviour | phenotype |
| smoking initiation | phenotype |
| smoking strata local | cohort |
| SNP_NCAM1_intron local | variant |
| SNP_trans_eQTL local | variant |
| Spirometry Data local | phenotype |
| substantia nigra | anatomy |
| target population | cohort |
| TBX5 local | gene |
| TET2 | gene |
| TEX41 local | gene |
| tobacco use | phenotype |
| TSEN54 local | gene |
| TSEN54 common variant local | variant |
| TTC12 | gene |
| UK10K | cohort |
| UK BiLEVE | cohort |
| UK BiLEVE array local | drug |
| UK Biobank | cohort |
| UK Biobank array local | drug |
| WDR61 local | gene |
| WHO Global Health Risks Report local | cohort |
| WNT3 | gene |
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