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Li D, Kim W, An J, Kim S, Lee S, Do A, Kim W, Lee S, Yoon D, Lee K, Ha S, Silverman EK, Cho M, Shin C, Won S. Heritability Analyses Uncover Shared Genetic Effects of Lung Function and Change over Time. Genes (Basel) 2022; 13:genes13071261. [PMID: 35886044 PMCID: PMC9316642 DOI: 10.3390/genes13071261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/05/2022] [Accepted: 07/08/2022] [Indexed: 01/27/2023] Open
Abstract
Genetic influence on lung functions has been identified in previous studies; however, the relative longitudinal effects of genetic factors and their interactions with smoking on lung function remain unclear. Here, we identified the longitudinal effects of genetic variants on lung function by determining single nucleotide polymorphism (SNP) heritability and genetic correlations, and by analyzing interactions with smoking. Subject-specific means and annual change rates were calculated for eight spirometric measures obtained from 6622 Korean adults aged 40−69 years every two years for 14 years, and their heritabilities were estimated separately. Statistically significant (p < 0.05) heritability for the subject-specific means of all spirometric measures (8~32%) and change rates of forced expiratory volume in 1 s to forced vital capacity ratio (FEV1/FVC; 16%) and post-bronchodilator FEV1/FVC (17%) were detected. Significant genetic correlations of the change rate with the subject-specific mean were observed for FEV1/FVC (ρg = 0.64) and post-bronchodilator FEV1/FVC (ρg = 0.47). Furthermore, post-bronchodilator FEV1/FVC showed significant heritability of SNP-by-smoking interaction (hGXS2 = 0.4) for the annual change rate. The GWAS also detected genome-wide significant SNPs for FEV1 (rs4793538), FEV1/FVC (rs2704589, rs62201158, and rs9391733), and post-bronchodilator FEV1/FVC (rs2445936). We found statistically significant evidence of heritability role on the change in lung function, and this was shared with the effects on cross-sectional measurements. We also found some evidence of interaction with smoking for the change of lung function.
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Affiliation(s)
- Donghe Li
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea; (D.L.); (A.D.)
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA
| | - Woojin Kim
- Department of Internal Medicine and Environmental Health Center, School of Medicine, Kangwon National University, Chuncheon 24341, Korea;
| | - Jahoon An
- Department of Public Health Science, Graduate School of Public Health, Seoul National University, Seoul 08826, Korea;
| | - Soriul Kim
- Institute for Human Genomic Study, College of Medicine, Korea University, Seoul 136701, Korea; (S.K.); (S.L.)
| | - Seungku Lee
- Institute for Human Genomic Study, College of Medicine, Korea University, Seoul 136701, Korea; (S.K.); (S.L.)
| | - Ahra Do
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea; (D.L.); (A.D.)
| | - Wonji Kim
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (W.K.); (E.K.S.); (M.C.)
| | - Sanghun Lee
- Department of Medical Consilience, Graduate School, Dankook University, Yongin 16890, Korea;
| | - Dankyu Yoon
- Division of Allergy and Respiratory Disease Research, Department of Chronic Disease Convergence Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea;
| | - Kwangbae Lee
- Korea Medical Institute, Seoul 03173, Korea; (K.L.); (S.H.)
| | - Seounguk Ha
- Korea Medical Institute, Seoul 03173, Korea; (K.L.); (S.H.)
| | - Edwin K. Silverman
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (W.K.); (E.K.S.); (M.C.)
| | - Michael Cho
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (W.K.); (E.K.S.); (M.C.)
| | - Chol Shin
- Institute for Human Genomic Study, College of Medicine, Korea University, Seoul 136701, Korea; (S.K.); (S.L.)
- Division of Pulmonary Sleep and Critical Care Medicine, Department of Internal Medicine, Korea University Ansan Hospital, Ansan 15355, Korea
- Correspondence: (C.S.); (S.W.)
| | - Sungho Won
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea; (D.L.); (A.D.)
- Department of Public Health Science, Graduate School of Public Health, Seoul National University, Seoul 08826, Korea;
- Institute of Health and Environment, Seoul National University, Seoul 08826, Korea
- RexSoft Inc., Seoul 08826, Korea
- Correspondence: (C.S.); (S.W.)
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Yamada M, Motoike IN, Kojima K, Fuse N, Hozawa A, Kuriyama S, Katsuoka F, Tadaka S, Shirota M, Sakurai M, Nakamura T, Hamanaka Y, Suzuki K, Sugawara J, Ogishima S, Uruno A, Kodama EN, Fujino N, Numakura T, Ichikawa T, Mitsune A, Ohe T, Kinoshita K, Ichinose M, Sugiura H, Yamamoto M. Genetic loci for lung function in Japanese adults with adjustment for exhaled nitric oxide levels as airway inflammation indicator. Commun Biol 2021; 4:1288. [PMID: 34782693 PMCID: PMC8593164 DOI: 10.1038/s42003-021-02813-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 10/27/2021] [Indexed: 11/08/2022] Open
Abstract
Lung function reflects the ability of the respiratory system and is utilized for the assessment of respiratory diseases. Because type 2 airway inflammation influences lung function, genome wide association studies (GWAS) for lung function would be improved by adjustment with an indicator of the inflammation. Here, we performed a GWAS for lung function with adjustment for exhaled nitric oxide (FeNO) levels in two independent Japanese populations. Our GWAS with genotype imputations revealed that the RNF5/AGER locus including AGER rs2070600 SNP, which introduces a G82S substitution of AGER, was the most significantly associated with FEV1/FVC. Three other rare missense variants of AGER were further identified. We also found genetic loci with three candidate genes (NOS2, SPSB2 and RIPOR2) associated with FeNO levels. Analyses with the BioBank-Japan GWAS resource revealed genetic links of FeNO and asthma-related traits, and existence of common genetic background for allergic diseases and their biomarkers. Our study identified the genetic locus most strongly associated with airway obstruction in the Japanese population and three genetic loci associated with FeNO, an indicator of type 2 airway inflammation in adults.
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Affiliation(s)
- Mitsuhiro Yamada
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ikuko N Motoike
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kaname Kojima
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Nobuo Fuse
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shu Tadaka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Matsuyuki Shirota
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Miyuki Sakurai
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Tomohiro Nakamura
- Department of Health Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yohei Hamanaka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kichiya Suzuki
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Junichi Sugawara
- Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Department of Health Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Akira Uruno
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Eiichi N Kodama
- Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Naoya Fujino
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tadahisa Numakura
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tomohiro Ichikawa
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ayumi Mitsune
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Ohe
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Department of System Bioinformatics, Tohoku University Graduate School of Information Sciences, Sendai, Japan
| | | | - Hisatoshi Sugiura
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.
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Zhu Z, Li J, Si J, Ma B, Shi H, Lv J, Cao W, Guo Y, Millwood IY, Walters RG, Lin K, Yang L, Chen Y, Du H, Yu B, Hasegawa K, Camargo CA, Moffatt MF, Cookson WOC, Chen J, Chen Z, Li L, Yu C, Liang L. A large-scale genome-wide association analysis of lung function in the Chinese population identifies novel loci and highlights shared genetic aetiology with obesity. Eur Respir J 2021; 58:2100199. [PMID: 33766948 PMCID: PMC8513692 DOI: 10.1183/13993003.00199-2021] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/02/2021] [Indexed: 01/25/2023]
Abstract
BACKGROUND Lung function is a heritable complex phenotype with obesity being one of its important risk factors. However, knowledge of their shared genetic basis is limited. Most genome-wide association studies (GWASs) for lung function have been based on European populations, limiting the generalisability across populations. Large-scale lung function GWASs in other populations are lacking. METHODS We included 100 285 subjects from the China Kadoorie Biobank (CKB). To identify novel loci for lung function, single-trait GWAS analyses were performed on forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and FEV1/FVC in the CKB. We then performed genome-wide cross-trait analysis between lung function and obesity traits (body mass index (BMI), BMI-adjusted waist-to-hip ratio and BMI-adjusted waist circumference) to investigate the shared genetic effects in the CKB. Finally, polygenic risk scores (PRSs) of lung function were developed in the CKB and their interaction with BMI's association on lung function were examined. We also conducted cross-trait analysis in parallel with the CKB using up to 457 756 subjects from the UK Biobank (UKB) for replication and investigation of ancestry-specific effects. RESULTS We identified nine genome-wide significant novel loci for FEV1, six for FVC and three for FEV1/FVC in the CKB. FEV1 and FVC showed significant negative genetic correlation with obesity traits in both the CKB and UKB. Genetic loci shared between lung function and obesity traits highlighted important biological pathways, including cell proliferation, embryo, skeletal and tissue development, and regulation of gene expression. Mendelian randomisation analysis suggested significant negative causal effects of BMI on FEV1 and on FVC in both the CKB and UKB. Lung function PRSs significantly modified the effect of change in BMI on change in lung function during an average follow-up of 8 years. CONCLUSION This large-scale GWAS of lung function identified novel loci and shared genetic aetiology between lung function and obesity. Change in BMI might affect change in lung function differently according to a subject's polygenic background. These findings may open new avenues for the development of molecular-targeted therapies for obesity and lung function improvement.
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Affiliation(s)
- Zhaozhong Zhu
- Program in Genetic Epidemiology and Statistical Genetics, Dept of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Dept of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- These four authors contributed equally to this article
| | - Jiachen Li
- Dept of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
- These four authors contributed equally to this article
| | - Jiahui Si
- Program in Genetic Epidemiology and Statistical Genetics, Dept of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Dept of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
- These four authors contributed equally to this article
| | - Baoshan Ma
- College of Information Science and Technology, Dalian Maritime University, Dalian, China
- These four authors contributed equally to this article
| | - Huwenbo Shi
- Program in Genetic Epidemiology and Statistical Genetics, Dept of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jun Lv
- Dept of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
- Key Laboratory of Molecular Cardiovascular Sciences (Peking University), Ministry of Education, Beijing, China
- Peking University Institute of Environmental Medicine, Beijing, China
| | - Weihua Cao
- Dept of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Yu Guo
- Chinese Academy of Medical Sciences, Beijing, China
| | - Iona Y Millwood
- Medical Research Council Population Health Research Unit at the University of Oxford, Oxford, UK
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Dept of Population Health, University of Oxford, Oxford, UK
| | - Robin G Walters
- Medical Research Council Population Health Research Unit at the University of Oxford, Oxford, UK
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Dept of Population Health, University of Oxford, Oxford, UK
| | - Kuang Lin
- Medical Research Council Population Health Research Unit at the University of Oxford, Oxford, UK
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Dept of Population Health, University of Oxford, Oxford, UK
| | - Ling Yang
- Medical Research Council Population Health Research Unit at the University of Oxford, Oxford, UK
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Dept of Population Health, University of Oxford, Oxford, UK
| | - Yiping Chen
- Medical Research Council Population Health Research Unit at the University of Oxford, Oxford, UK
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Dept of Population Health, University of Oxford, Oxford, UK
| | - Huaidong Du
- Medical Research Council Population Health Research Unit at the University of Oxford, Oxford, UK
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Dept of Population Health, University of Oxford, Oxford, UK
| | - Bo Yu
- NCDs Prevention and Control Dept, Nangang CDC, Harbin, China
| | - Kohei Hasegawa
- Dept of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Carlos A Camargo
- Program in Genetic Epidemiology and Statistical Genetics, Dept of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Dept of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Miriam F Moffatt
- Section of Genomic Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - William O C Cookson
- Section of Genomic Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Junshi Chen
- China National Center for Food Safety Risk Assessment, Beijing, China
| | - Zhengming Chen
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Dept of Population Health, University of Oxford, Oxford, UK
| | - Liming Li
- Dept of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Canqing Yu
- Dept of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
- These two authors contributed equally to this article as lead authors and supervised the work
| | - Liming Liang
- Program in Genetic Epidemiology and Statistical Genetics, Dept of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Dept of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- These two authors contributed equally to this article as lead authors and supervised the work
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Lee KS, Kim KH, Oh YM, Han B, Kim WJ. A genome wide association study for lung function in the Korean population using an exome array. Korean J Intern Med 2021; 36:S142-S150. [PMID: 32336055 PMCID: PMC8009153 DOI: 10.3904/kjim.2019.204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 01/09/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND/AIMS Lung function is an objective indicator of diagnosis and prognosis of respiratory diseases. Many common genetic variants have been associated with lung function in multiple ethnic populations. We looked for coding variants associated with forced expiratory volume in 1 second (FEV1) and FEV1/forced vital capacity (FVC) in the Korean general population. METHODS We carried out exome array analysis and lung function measurements of the FEV1 and FEV1/FVC in 7,524 individuals of the Korean population. We evaluated single variants with minor allele frequency greater than 0.5%. We performed look-ups for candidate coding variants associations in the UK Biobank, SpiroMeta, and CHARGE consortia. RESULTS We identified coding variants in the SMIM29 (C6orf1) (p = 1.2 × 10-5) and HMGA1 locus on chromosome 6p21, the GIT2 (p = 6.5 × 10-5) locus on chromosome 12q24, and the ARHGEF40 (p = 9.9 × 10-5) locus on chromosome 14q11 as having a significant association with lung function (FEV1). We also confirmed a previously reported association with lung function and chronic obstructive pulmonary disease in the FAM13A (p = 4.54 × 10-6) locus on chromosome 4q22, in TNXB (p = 1.30 × 10-6) and in AGER (p = 1.09 × 10-8) locus on chromosome 6p21. CONCLUSION Our exome array analysis identified that several protein coding variants were associated with lung function in the Korean population. Common coding variants in SMIM29 (C6orf1), HMGA1, GIT2, FAM13A, TNXB, AGER and low-frequency variant in ARHGEF40 potentially affect lung function, which warrant further study.
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Affiliation(s)
- Kyu-Sun Lee
- Department of Internal Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
| | - Kun Hee Kim
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Yeon-Mok Oh
- Department of Pulmonary and Critical Care Medicine and Clinical Research Center for Chronic Obstructive Airway Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Buhm Han
- Department of Medical Science, Seoul National University College of Medicine, Seoul, Korea
| | - Woo Jin Kim
- Department of Internal Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
- Correspondence to Woo Jin Kim, M.D. Department of Internal Medicine, Kangwon National University School of Medicine, 156 Baengnyeong-ro, Chuncheon 24289, Korea Tel: +82-33-250-7815 Fax: +82-33-255-6567 E-mail:
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Park B, An J, Kim W, Kang HY, Koh SB, Oh B, Jung KJ, Jee SH, Kim WJ, Cho MH, Silverman EK, Park T, Won S. Effect of 6p21 region on lung function is modified by smoking: a genome-wide interaction study. Sci Rep 2020; 10:13075. [PMID: 32753590 PMCID: PMC7403370 DOI: 10.1038/s41598-020-70092-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 07/15/2020] [Indexed: 11/10/2022] Open
Abstract
Smoking is a major risk factor for chronic obstructive pulmonary disease (COPD); however, more than 25% of COPD patients are non-smokers, and gene-by-smoking interactions are expected to affect COPD onset. We aimed to identify the common genetic variants interacting with pack-years of smoking on FEV1/FVC ratios in individuals with normal lung function. A genome-wide interaction study (GWIS) on FEV1/FVC was performed for individuals with FEV1/FVC ratio ≥ 70 in the Korea Associated Resource cohort data, and significant SNPs were validated using data from two other Korean cohorts. The GWIS revealed that rs10947231 and rs8192575 met genome-wide significant levels; For \documentclass[12pt]{minimal}
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\begin{document}$${\text{H}}_{0} :\beta_{SNP} = \beta_{SNP*pack - years} = 0{\text{ vs H}}_{1} : not {\text{H}}_{0} ,$$\end{document}H0:βSNP=βSNP∗pack-years=0vs H1:notH0, the likelihood ratio (LR) test was conducted, and its P values, PLR, for rs10947231 and rs8192575 were 2.23 × 10–12 and 1.18 × 10–8, respectively. Interaction between rs8192575 and smoking is significantly replicated with two additional data (PINT = 0.0454, 0.0131). Expression quantitative trait loci, topologically associated domains, and PrediXcan analyses revealed that rs8192575 is significantly associated with AGER expression. SNPs on the 6p21 region are associated with FEV1/FVC, and the effect of smoking on FEV1/FVC differs among the associated genotypes.
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Affiliation(s)
- Boram Park
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea
| | - Jaehoon An
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea
| | - Wonji Kim
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea
| | - Hae Yeon Kang
- Department of Internal Medicine, Healthcare Research Institute, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, South Korea
| | - Sang Baek Koh
- Department of Preventive Medicine, Yonsei University Wonju College of Medicine, Wonju, South Korea
| | - Bermseok Oh
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, South Korea
| | - Keum Ji Jung
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Sun Ha Jee
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center, Kangwon National University Hospital, School of Medicine, Kangwon University, Chuncheon, South Korea
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Taesung Park
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea. .,Department of Statistics, Seoul National University, Seoul, South Korea.
| | - Sungho Won
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea. .,Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea. .,Institute of Health and Environment, Seoul National University, Seoul, South Korea.
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The correlation between CYP4F2 variants and chronic obstructive pulmonary disease risk in Hainan Han population. Respir Res 2020; 21:86. [PMID: 32295578 PMCID: PMC7161254 DOI: 10.1186/s12931-020-01348-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 04/01/2020] [Indexed: 01/19/2023] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is a complex pulmonary disease. Cytochrome P450 family 4 subfamily F member 2 (CYP4F2) belongs to cytochrome P450 superfamily of enzymes responsible for metabolism, its single nucleotide polymorphisms (SNPs) were reported to be involved in metabolism in the development of many diseases. The study aimed to assess the relation between CYP4F2 SNPs and COPD risk in the Hainan Han population. Method We genotyped five SNPs in CYP4F2 in 313 cases and 508 controls by Agena MassARRAY assay. The association between CYP4F2 SNPs and COPD risk were assessed by χ2 test and genetic models. Besides, logistic regression analysis was introduced into the calculation for odds ratio (OR) and 95% confidence intervals (CIs). Results Allele model analysis indicated that rs3093203 A was significantly correlated with an increased risk of COPD. Also, rs3093193 G and rs3093110 G were associated with a reduced COPD risk. In the genetic models, we found that rs3093203 was related to an increased COPD risk, while rs3093193 and rs3093110 were related to a reduced risk of COPD. After gender stratification, rs3093203, rs3093193 and rs3093110 showed the association with COPD risk in males. With smoking stratification, rs3093144 was significantly associated with an increased risk of COPD in smokers. CYP4F2 SNPs were significantly associated with COPD risk. Conclusions Our findings illustrated potential associations between CYP4F2 polymorphisms and COPD risk. However, large-scale and well-designed studies are needed to determine conclusively the association between the CYP4F2 SNPs and COPD risk.
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Trade-offs in aging lung diseases: a review on shared but opposite genetic risk variants in idiopathic pulmonary fibrosis, lung cancer and chronic obstructive pulmonary disease. Curr Opin Pulm Med 2019. [PMID: 29517586 PMCID: PMC5895171 DOI: 10.1097/mcp.0000000000000476] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW The process of aging involves biological changes that increases susceptibility for disease. In the aging lung disease IPF, GWAS studies identified genes associated with risk for disease. Recently, several of these genes were also found to be involved in risk for COPD or lung cancer. This review describes GWAS-derived risk genes for IPF that overlap with risk genes for lung cancer or COPD. RECENT FINDINGS Risk genes that overlap between aging lung diseases, include FAM13A, DSP and TERT. Most interestingly, disease predisposing alleles for IPF are opposite to those for COPD or lung cancer. Studies show that the alleles are associated with differential gene expression and with physiological traits in the general population. The opposite allelic effect sizes suggest the presence of trade-offs in the aging lung. For TERT, the trade-off involves cellular senescence versus proliferation and repair. For FAM13A and DSP, trade-offs may involve protection from noxious gases or tissue integrity. SUMMARY The overlap in risk genes in aging lung diseases provides evidence that processes associated with FAM13A, DSP and TERT are important for healthy aging. The opposite effect size of the disease risk alleles may represent trade-offs, for which a model involving an apicobasal gene expression gradient is presented.
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The rs2609255 polymorphism in the FAM13A gene is reproducibly associated with silicosis susceptibility in a Chinese population. Gene 2018; 661:196-201. [DOI: 10.1016/j.gene.2018.03.098] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/22/2018] [Accepted: 03/29/2018] [Indexed: 12/21/2022]
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Association of nsv823469 copy number loss with decreased risk of chronic obstructive pulmonary disease and pulmonary function in Chinese. Sci Rep 2017; 7:40060. [PMID: 28079130 PMCID: PMC5227687 DOI: 10.1038/srep40060] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/30/2016] [Indexed: 01/17/2023] Open
Abstract
It is highly possible that copy number variations (CNVs) in susceptible regions have effects on chronic obstructive pulmonary disease (COPD) development, while long noncoding RNA (lncRNAs) have been shown to cause COPD. We hypothesized that the common CNV, named nsv823469 located on 6p22.1, and covering lncRNAs (major histocompatibility complex, class I, A (HLA-A) and HLA complex group 4B (HCG4B)) has an effect on COPD risk. This association was assessed through a two-stage case-control study, and was further confirmed with COPD and pulmonary function-based family analyses, respectively. The copy number loss (0-copy/1-copy) of nsv823469 significantly decreased risk of COPD compared with normal (2-copy) (OR = 0.77, 95% CI = 0.69–0.85). The loss allele, inducing copy number loss of nsv823469, has a tendency to transmit to offspring or siblings (P = 0.010) and is associated with forced expiratory volume in 1 second (FEV1) (P = 0.030). Furthermore, the copy number loss of nsv823469 in normal pulmonary tissue decreases the expression levels of HCG4B (r = 0.315, P = 0.031) and HLA-A (r = 0.296, P = 0.044). Our data demonstrates that nsv823469 plays a role in COPD and pulmonary function inheritance by potentially altering expression of HCG4B.
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10
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Ding Y, Niu H, Zhou L, Zhou W, Chen J, Xie S, Geng T, Ouyang Y, He P, Sun P, Feng T, Jin T. Association of multiple genetic variants with chronic obstructive pulmonary disease susceptibility in Hainan region. CLINICAL RESPIRATORY JOURNAL 2015; 11:727-732. [PMID: 26502206 DOI: 10.1111/crj.12407] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 09/07/2015] [Accepted: 10/17/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Yipeng Ding
- Department of Emergency; People's Hospital of Hainan Province; Haikou Hainan 570311 China
| | - Huan Niu
- Department of Emergency; People's Hospital of Hainan Province; Haikou Hainan 570311 China
| | - Long Zhou
- School of Life Sciences; Northwest University; Xi'an 710069 China
| | - Wenjing Zhou
- School of Life Sciences; Northwest University; Xi'an 710069 China
| | - Jiannan Chen
- Department of Emergency; People's Hospital of Hainan Province; Haikou Hainan 570311 China
| | - Shiliang Xie
- Department of Respiration; People's Hospital of Lingao; Lingao Hainan 571400 China
| | - Tingting Geng
- National Engineering Research Center for Miniaturized Detection Systems; Xi'an 710069 China
| | - Yanhong Ouyang
- Department of Emergency; People's Hospital of Hainan Province; Haikou Hainan 570311 China
| | - Ping He
- Department of Emergency; People's Hospital of Hainan Province; Haikou Hainan 570311 China
| | - Pei Sun
- Department of Emergency; People's Hospital of Hainan Province; Haikou Hainan 570311 China
| | - Tian Feng
- National Engineering Research Center for Miniaturized Detection Systems; Xi'an 710069 China
| | - Tianbo Jin
- School of Life Sciences; Northwest University; Xi'an 710069 China
- National Engineering Research Center for Miniaturized Detection Systems; Xi'an 710069 China
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11
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Abstract
COPD is a common complex disease characterized by progressive airflow limitation. Several genome-wide association studies (GWASs) have discovered genes that are associated with COPD. Recently, candidate genes for COPD identified by GWASs include CHRNA3/5 (cholinergic nicotine receptor alpha 3/5), IREB2 (iron regulatory binding protein 2), HHIP (hedgehog-interacting protein), FAM13A (family with sequence similarity 13, member A), and AGER (advanced glycosylation end product–specific receptor). Their association with COPD susceptibility has been replicated in multiple populations. Since these candidate genes have not been considered in COPD, their pathological roles are still largely unknown. Herein, we review some evidences that they can be effective drug targets or serve as biomarkers for diagnosis or subtyping. However, more study is required to understand the functional roles of these candidate genes. Future research is needed to characterize the effect of genetic variants, validate gene function in humans and model systems, and elucidate the genes’ transcriptional and posttranscriptional regulatory mechanisms.
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Affiliation(s)
- Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center, Kangwon National University, Chuncheon, South Korea
| | - Sang Do Lee
- Department of Pulmonary and Critical Care Medicine, Clinical Research Center for Chronic Obstructive Airway Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
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12
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Family-Based Association Study of Pulmonary Function in a Population in Northeast Asia. PLoS One 2015; 10:e0139716. [PMID: 26430897 PMCID: PMC4592257 DOI: 10.1371/journal.pone.0139716] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 09/15/2015] [Indexed: 12/22/2022] Open
Abstract
The spirometric measurement of pulmonary function by measuring the forced expiratory volume in one second (FEV1) is a heritable trait that reflects the physiological condition of the lung and airways. Genome-wide linkage and association studies have identified a number of genes and genetic loci associated with pulmonary function. However, limited numbers of studies have been reported for Asian populations. In this study, we aimed to investigate genetic evidence of pulmonary function in a population in northeast Asia. We conducted a family-based association test with 706 GENDISCAN study participants from 72 Mongolian families to determine candidate genetic determinants of pulmonary function. For the replication, we chose seven candidate single nucleotide polymorphisms (SNPs) from the 5 loci, and tested 1062 SNPs for association with FEV1 from 2,729 subjects of the Korea Healthy Twin study. We identified TMEM132C as a potential candidate gene at 12q24.3, which is a previously reported locus of asthma and spirometric indices. We also found two adjacent candidate genes (UNC93A and TTLL2) in the 6q27 region, which has been previously identified as a pulmonary function locus in the Framingham cohort study. Our findings suggest that novel candidate genes (TMEM132C, UNC93A and TTLL2) in two different regions are associated with pulmonary function in a population in northeast Asia.
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13
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Kim BH, Kim HN, Roh SJ, Lee MK, Yang S, Lee SK, Sung YA, Chung HW, Cho NH, Shin C, Sung J, Kim HL. GWA meta-analysis of personality in Korean cohorts. J Hum Genet 2015; 60:455-60. [PMID: 25994864 DOI: 10.1038/jhg.2015.52] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 03/06/2015] [Accepted: 04/08/2015] [Indexed: 12/11/2022]
Abstract
Personality is a determinant of behavior and lifestyle that is associated with health and human diseases. Despite the heritability of personality traits is well established, the understanding of the genetic contribution to personality trait variation is extremely limited. To identify genetic variants associated with each of the five dimensions of personality, we performed a genome-wide association (GWA) meta-analysis of three cohorts, followed by comparison of a family cohort. Personality traits were measured with the Revised NEO Personality Inventory for the five-factor model (FFM) of personality. We investigated the top five single-nucleotide polymorphisms (SNPs) for each trait, and revealed the most highly association with neuroticism and TACC2 (rs1010657, P=8.79 × 10(-7)), extraversion and PTPN12 (rs12537271, P=1.47 × 10(-7)), openness and IMPAD1 (rs16921695, P=5 × 10(-8)), agreeableness and RPS29 (rs8015351, P=1.27 × 10(-6)) and conscientiousness and LMO4 (rs912765, P=2.91 × 10(-6)). It had no SNP reached the GWA study threshold (P<5 × 10(-8)). When expanded the SNPs up to top 100, the correlation of PTPRD (rs1029089) and agreeableness was confirmed in Healthy Twin cohort with other 13 SNPs. This GWA meta-analysis on FFM personality traits is meaningful as it was the first on a non-Caucasian population targeted to FFM of personality traits.
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Affiliation(s)
- Bo-Hye Kim
- Department of Biochemistry, School of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Han-Na Kim
- Department of Biochemistry, School of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Seung-Ju Roh
- Department of Biochemistry, School of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Mi Kyeong Lee
- Complex Disease and Genetic Epidemiology Branch, Department of Epidemiology and Institute of Environment and Health, School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Sarah Yang
- Complex Disease and Genetic Epidemiology Branch, Department of Epidemiology and Institute of Environment and Health, School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Seung Ku Lee
- Institute of Human Genomic Study, Korea University Ansan Hospital, Ansan, Republic of Korea
| | - Yeon-Ah Sung
- Department of Internal Medicine, School of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Hye Won Chung
- Department of Obstetrics and Gynecology, School of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Nam H Cho
- Department of Preventive Medicine, School of Medicine, Ajou University, Suwon, Republic of Korea
| | - Chol Shin
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Korea University Hospital, Ansan, Republic of Korea
| | - Joohon Sung
- Complex Disease and Genetic Epidemiology Branch, Department of Epidemiology and Institute of Environment and Health, School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Hyung-Lae Kim
- Department of Biochemistry, School of Medicine, Ewha Womans University, Seoul, Republic of Korea
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14
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Kim S, Kim H, Cho N, Lee SK, Han BG, Sull JW, Jee SH, Shin C. Identification of FAM13A gene associated with the ratio of FEV1 to FVC in Korean population by genome-wide association studies including gene-environment interactions. J Hum Genet 2015; 60:139-45. [PMID: 25608829 DOI: 10.1038/jhg.2014.118] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/28/2014] [Accepted: 12/09/2014] [Indexed: 01/12/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a complex, multifactorial disease. Although smoking is a main risk factor for obstructive impairment, not all smokers develop this critical disease. We conducted a genome-wide association study to identify the association between genetic variants and pulmonary function and also examined how these variants relate to lung impairment in accordance with smoking behaviors. Using two community-based cohorts, the Ansan cohort (n=4319) and the Ansung cohort (n=3674), in the Korean Genome Epidemiology Study, we analyzed the association between genetic variants (single-nucleotide polymorphisms and haplotypes) and the ratio of FEV1 to FVC (FEV1/FVC) using multivariate linear regression models. Similar analyses were conducted after stratification by smoking status. Four genome-wide significant signals in the FAM13A gene (the strongest signal at rs2609264, P=1.76 × 10(-7) in a combined set) were associated with FEV1/FVC. For the association with ratio, the effect size in the CTGA haplotype (risk haplotype) was -0.57% (s.e., 0.11; P=2.10 × 10(-7)) as compared with the TCAG haplotype (reference haplotype) in a combined set. There was also a significant interaction of FAM13A haplotypes with heavy smoking on FEV1/FVC (P for interaction=0.028). We confirmed the previously reported association of FAM13A in 4q22.1 with pulmonary function. The FAM13A haplotypes also interacted with heavy smoking to affect the risk of reduced pulmonary function.
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Affiliation(s)
- Soriul Kim
- 1] Institute of Human Genomic Study, Ansan Hospital, Korea University, Ansan, Republic of Korea [2] Department of Public Health, Graduate School, Yonsei University, Seoul, Republic of Korea
| | - Hyun Kim
- Institute of Human Genomic Study, Ansan Hospital, Korea University, Ansan, Republic of Korea
| | - Namhan Cho
- Department of Preventive Medicine, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Seung Ku Lee
- Institute of Human Genomic Study, Ansan Hospital, Korea University, Ansan, Republic of Korea
| | - Bok-Ghee Han
- Center for Genome Science, National Institute of Health, Cheongwon, Republic of Korea
| | - Jae Woong Sull
- Department of Bio-Medical Laboratory Science, College of Health Science, Eulji University, Sungnam, Republic of Korea
| | - Sun Ha Jee
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Republic of Korea
| | - Chol Shin
- 1] Institute of Human Genomic Study, Ansan Hospital, Korea University, Ansan, Republic of Korea [2] Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Korea University Ansan Hospital, Ansan, Republic of Korea
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15
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Corvol H, Hodges CA, Drumm ML, Guillot L. Moving beyond genetics: is FAM13A a major biological contributor in lung physiology and chronic lung diseases? J Med Genet 2014; 51:646-9. [PMID: 25163686 DOI: 10.1136/jmedgenet-2014-102525] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Variants in FAM13A have been found in genome-wide association studies (GWAS) to associate with lung function in the general population as well as in several common chronic lung diseases (CLD) such as chronic obstructive pulmonary disease (COPD), asthma, as well as in idiopathic interstitial pneumonias (IIP). The gene was cloned in 2004, yet the encoded protein has not been characterised and its function is unknown. The redundancy of its genetic contribution in CLD suggests a major function of this gene both in lung physiology and CLD. This review provides a brief summary of the current knowledge of FAM13A, and demonstrates the necessity to resolve its biological function besides its well accepted genetic contribution. Further interpretations of FAM13A variants may help in the understanding of CLD mechanisms and reveal opportunity for intervention.
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Affiliation(s)
- Harriet Corvol
- INSERM, UMR_S 938, CDR Saint-Antoine, Paris, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, Paris, France Pneumologie pédiatrique, APHP, Hôpital Trousseau, Paris, France
| | - Craig A Hodges
- Department of Pediatrics, Case Western Reserve University, Cleveland, Ohio, USA Department of Genetics and Genome Sciences, Case Western University, Cleveland, Ohio, USA
| | - Mitchell L Drumm
- Department of Pediatrics, Case Western Reserve University, Cleveland, Ohio, USA Department of Genetics and Genome Sciences, Case Western University, Cleveland, Ohio, USA
| | - Loïc Guillot
- INSERM, UMR_S 938, CDR Saint-Antoine, Paris, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, Paris, France
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16
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Association of Lung Function Genes with Chronic Obstructive Pulmonary Disease. Lung 2014; 192:473-80. [DOI: 10.1007/s00408-014-9579-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 03/21/2014] [Indexed: 10/25/2022]
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