Targeted sequencing of lung function loci in chronic obstructive pulmonary disease cases and controls

PLoS ONE

Volumn 12, Issue 1, 2017, Pages

  Artigas, María Soler ^a   Wain, Louise V ^a,b   Shrine, Nick ^a   McKeever, Tricia M ^c   Bileve, U K ^d   Sayers, Ian ^c   Hall, Ian P ^c   Tobin, Martin D ^a,b  

^a UNIVERSITY OF LEICESTER   (United Kingdom)

^b GLENFIELD HOSPITAL   (United Kingdom)

^c UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^d NONE

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; BIOBANK; CHRONIC OBSTRUCTIVE LUNG DISEASE; CONTROLLED STUDY; GENE; GENE FREQUENCY; GENE LOCUS; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC ASSOCIATION; GENETIC RISK; GENETIC VARIABILITY; HERITABILITY; HHIP GENE; HUMAN; LUNG FUNCTION; MAJOR CLINICAL STUDY; MECOM GENE; TNXB GENE; CASE CONTROL STUDY; GENETICS; LUNG FUNCTION TEST; PATHOPHYSIOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

ADULT; CASE-CONTROL STUDIES; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; PULMONARY DISEASE, CHRONIC OBSTRUCTIVE; RESPIRATORY FUNCTION TESTS;

EID: 85010433812     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0170222     Document Type: Article

References (53)

1. Lozano R, Naghavi M, Foreman K, Lim S, Shibuya K, Aboyans V, et al. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet. 2012;380(9859):2095-128. Epub 2012/12/19. doi:10.1016/S0140-6736 (12) 61728-0 PMID: 23245604
2. Abbey DE, Burchette RJ, Knutsen SF, McDonnell WF, Lebowitz MD, Enright PL. Long-term particulate and other air pollutants and lung function in nonsmokers. American journal of respiratory and critical care medicine. 1998;158(1):289-98. Epub 1998/07/09. doi:10.1164/ajrccm.158.1.9710101 PMID: 9655742
3. Global Initiative for Chronic Obstructive Lung Disease (GOLD). Global Strategy for the Diagnosis, Management and Prevention of COPD 2014. http://www.goldcopd.org/.
4. Ingebrigtsen T, Thomsen SF, Vestbo J, van der Sluis S, Kyvik KO, Silverman EK, et al. Genetic influences on Chronic Obstructive Pulmonary Disease-a twin study. Respiratory medicine. 2010;104(12):1890-5. Epub 2010/06/15. doi:10.1016/j.rmed.2010.05.004 PMID: 20541380
5. Palmer LJ, Knuiman MW, Divitini ML, Burton PR, James AL, Bartholomew HC, et al. Familial aggregation and heritability of adult lung function: results from the Busselton Health Study. The European respiratory journal: official journal of the European Society for Clinical Respiratory Physiology. 2001;17(4):696-702. Epub 2001/06/13.
6. Lewitter FI, Tager IB, McGue M, Tishler PV, Speizer FE. Genetic and environmental determinants of level of pulmonary function. American journal of epidemiology. 1984;120(4):518-30. Epub 1984/10/01. PMID: 6475921
7. Repapi E, Sayers I, Wain LV, Burton PR, Johnson T, Obeidat M, et al. Genome-wide association study identifies five loci associated with lung function. Nature genetics. 2010;42(1):36-44. doi:10.1038/ng. 501 PMID: 20010834
8. Wilk JB, Chen TH, Gottlieb DJ, Walter RE, Nagle MW, Brandler BJ, et al. A genome-wide association study of pulmonary function measures in the Framingham Heart Study. PLoS Genet. 2009;5(3):e1000429. Epub 2009/03/21. doi:10.1371/journal.pgen. 1000429 PMID: 19300500
9. Soler Artigas M, Loth DW, Wain LV, Gharib SA, Obeidat M, Tang W, et al. Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function. Nature genetics. 2011;43(11):1082-90. Epub 2011/09/29. doi:10.1038/ng.941 PMID: 21946350
10. Hancock DB, Eijgelsheim M, Wilk JB, Gharib SA, Loehr LR, Marciante KD, et al. Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function. Nature genetics. 2010;42(1):45-52. doi:10.1038/ng.500 PMID: 20010835
11. Wain LV, Shrine N, Miller S, Jackson VE, Ntalla I, Artigas MS, et al. 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. 2015;3(10):769-81. Epub 2015/10/02. doi:10.1016/S2213-2600 (15) 00283-0 PMID: 26423011
12. Soler Artigas M, Wain LV, Miller S, Kheirallah AK, Huffman JE, Ntalla I, et al. Sixteen new lung function signals identified through 1000 Genomes Project reference panel imputation. Nature communications. 2015;6:8658. Epub 2015/12/05. doi:10.1038/ncomms9658 PMID: 26635082
13. Cho MH, Boutaoui N, Klanderman BJ, Sylvia JS, Ziniti JP, Hersh CP, et al. Variants in FAM13A are associated with chronic obstructive pulmonary disease. Nature genetics. 2010;42(3):200-2. doi:10. 1038/ng.535 PMID: 20173748
14. Cho MH, McDonald ML, Zhou X, Mattheisen M, Castaldi PJ, Hersh CP, et al. Risk loci for chronic obstructive pulmonary disease: a genome-wide association study and meta-analysis. The Lancet Respiratory medicine. 2014;2(3):214-25. Epub 2014/03/14. doi:10.1016/S2213-2600 (14) 70002-5 PMID: 24621683
15. Pillai SG, Ge D, Zhu G, Kong X, Shianna KV, Need AC, et al. A genome-wide association study in chronic obstructive pulmonary disease (COPD): identification of two major susceptibility loci. PLoS Genet. 2009;5(3):e1000421. Epub 2009/03/21. doi:10.1371/journal.pgen. 1000421 PMID: 19300482
16. Wilk JB, Shrine NR, Loehr LR, Zhao JH, Manichaikul A, Lopez LM, et al. Genome-wide association studies identify CHRNA5/3 and HTR4 in the development of airflow obstruction. American journal of respiratory and critical care medicine. 2012;186(7):622-32. Epub 2012/07/28. doi:10.1164/rccm. 201202-0366OC PMID: 22837378
17. Castaldi PJ, Cho MH, Litonjua AA, Bakke P, Gulsvik A, Lomas DA, et al. The Association of Genome-Wide Significant Spirometric Loci with COPD Susceptibility. Am J Respir Cell Mol Biol. 2011. Epub 2011/06/11.
18. Soler Artigas M, Wain LV, Repapi E, Obeidat M, Sayers I, Burton PR, et al. Effect of five genetic variants associated with lung function on the risk of chronic obstructive lung disease, and their joint effects on lung function. American journal of respiratory and critical care medicine. 2011;184(7):786-95. Epub 2011/10/04. doi:10.1164/rccm.201102-0192OC PMID: 21965014
19. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, et al. Finding the missing heritability of complex diseases. Nature. 2009;461(7265):747-53. Epub 2009/10/09. doi:10.1038/nature08494 PMID: 19812666
20. 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, et al. An integrated map of genetic variation from 1, 092 human genomes. Nature. 2012;491(7422):56-65. Epub 2012/11/07. doi:10.1038/nature11632 PMID: 23128226
21. UK10K Consortium, Walter K, Min JL, Huang J, Crooks L, Memari Y, et al. The UK10K project identifies rare variants in health and disease. Nature. 2015;526(7571):82-90. Epub 2015/09/15. doi:10.1038/nature14962 PMID: 26367797
22. Stewart CE, Hall IP, Parker SG, Moffat MF, Wardlaw AJ, Connolly MJ, et al. PLAUR polymorphisms and lung function in UK smokers. BMC medical genetics. 2009;10:112. doi:10.1186/1471-2350-10-112 PMID: 19878584
23. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754-60. doi:10.1093/bioinformatics/btp324 PMID: 19451168
24. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078-9. doi:10.1093/bioinformatics/btp352 PMID: 19505943
25. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome research. 2010;20(9):1297-303. Epub 2010/07/21. doi:10.1101/gr.107524.110 PMID: 20644199
26. Altmann A, Weber P, Quast C, Rex-Haffner M, Binder EB, Muller-Myhsok B. vipR: variant identification in pooled DNA using R. Bioinformatics. 2011;27(13):i77-84. Epub 2011/06/21. doi:10.1093/bioinformatics/btr205 PMID: 21685105
27. Wei Z, Wang W, Hu P, Lyon GJ, Hakonarson H. SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data. Nucleic acids research. 2011;39(19):e132. Epub 2011/08/05. doi:10.1093/nar/gkr599 PMID: 21813454
28. Rivas MA, Beaudoin M, Gardet A, Stevens C, Sharma Y, Zhang CK, et al. Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nature genetics. 2011;43(11):1066-73. Epub 2011/10/11. doi:10.1038/ng.952 PMID: 21983784
29. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, et al. dbSNP: the NCBI database of genetic variation. Nucleic acids research. 2001;29(1):308-11. PMID: 11125122
30. Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, Pittard WS, et al. An initial map of insertion and deletion (INDEL) variation in the human genome. Genome research. 2006;16(9):1182-90. doi:10. 1101/gr.4565806 PMID: 16902084
31. Neale BM, Rivas MA, Voight BF, Altshuler D, Devlin B, Orho-Melander M, et al. Testing for an unusual distribution of rare variants. PLoS Genet. 2011;7(3):e1001322. doi:10.1371/journal.pgen. 1001322 PMID: 21408211
32. Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, et al. ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic acids research. 2013;41(Database issue):D56-63. doi:10.1093/nar/gks1172 PMID: 23193274
33. Hwang JY, Lee SH, Go MJ, Kim BJ, Kou I, Ikegawa S, et al. Meta-analysis identifies a MECOM gene as a novel predisposing factor of osteoporotic fracture. Journal of medical genetics. 2013;50(4):212-9. doi:10.1136/jmedgenet-2012-101156 PMID: 23349225
34. Okada Y, Sim X, Go MJ, Wu JY, Gu D, Takeuchi F, et al. Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations. Nature genetics. 2012;44(8):904-9. doi:10.1038/ng.2352 PMID: 22797727
35. Bei JX, Li Y, Jia WH, Feng BJ, Zhou G, Chen LZ, et al. A genome-wide association study of nasopharyngeal carcinoma identifies three new susceptibility loci. Nature genetics. 2010;42(7):599-603. Epub 2010/06/01. doi:10.1038/ng.601 PMID: 20512145
36. Wain LV, Verwoert GC, O'Reilly PF, Shi G, Johnson T, Johnson AD, et al. Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure. Nature genetics. 2011;43(10):1005-11. Epub 2011/09/13. doi:10.1038/ng.922 PMID: 21909110
37. Meyer TE, Verwoert GC, Hwang SJ, Glazer NL, Smith AV, van Rooij FJ, et al. Genome-wide association studies of serum magnesium, potassium, and sodium concentrations identify six Loci influencing serum magnesium levels. PLoS Genet. 2010;6(8). Epub 2010/08/12.
38. Bard-Chapeau EA, Szumska D, Jacob B, Chua BQ, Chatterjee GC, Zhang Y, et al. Mice carrying a hypomorphic Evi1 allele are embryonic viable but exhibit severe congenital heart defects. PloS one. 2014;9(2):e89397. Epub 2014/03/04. doi:10.1371/journal.pone.0089397 PMID: 24586749
39. Choi YW, Choi JS, Zheng LT, Lim YJ, Yoon HK, Kim YH, et al. Comparative genomic hybridization array analysis and real time PCR reveals genomic alterations in squamous cell carcinomas of the lung. Lung cancer. 2007;55(1):43-51. Epub 2006/11/18. doi:10.1016/j.lungcan. 2006.09.018 PMID: 17109992
40. Starr TK, Allaei R, Silverstein KA, Staggs RA, Sarver AL, Bergemann TL, et al. A transposon-based genetic screen in mice identifies genes altered in colorectal cancer. Science. 2009;323(5922):1747-50. Epub 2009/03/03. doi:10.1126/science.1163040 PMID: 19251594
41. Yokoi S, Yasui K, Iizasa T, Imoto I, Fujisawa T, Inazawa J. TERC identified as a probable target within the 3q26 amplicon that is detected frequently in non-small cell lung cancers. Clinical cancer research: an official journal of the American Association for Cancer Research. 2003;9(13):4705-13. Epub 2003/10/29.
42. Goyama S, Yamamoto G, Shimabe M, Sato T, Ichikawa M, Ogawa S, et al. Evi-1 is a critical regulator for hematopoietic stem cells and transformed leukemic cells. Cell stem cell. 2008;3(2):207-20. Epub 2008/08/07. doi:10.1016/j.stem.2008.06.002 PMID: 18682242
43. Yuasa H, Oike Y, Iwama A, Nishikata I, Sugiyama D, Perkins A, et al. Oncogenic transcription factor Evi1 regulates hematopoietic stem cell proliferation through GATA-2 expression. The EMBO journal. 2005;24(11):1976-87. Epub 2005/05/13. doi:10.1038/sj.emboj.7600679 PMID: 15889140
44. Hoyt PR, Bartholomew C, Davis AJ, Yutzey K, Gamer LW, Potter SS, et al. The Evi1 proto-oncogene is required at midgestation for neural, heart, and paraxial mesenchyme development. Mechanisms of development. 1997;65(1-2):55-70. Epub 1997/07/01. PMID: 9256345
45. Zhou X, Baron RM, Hardin M, Cho MH, Zielinski J, Hawrylkiewicz I, et al. Identification of a chronic obstructive pulmonary disease genetic determinant that regulates HHIP. Human molecular genetics. 2012;21(6):1325-35. doi:10.1093/hmg/ddr569 PMID: 22140090
46. Chen X, Listman JB, Slack FJ, Gelernter J, Zhao H. Biases and errors on allele frequency estimation and disease association tests of next-generation sequencing of pooled samples. Genet Epidemiol. 2012;36(6):549-60. doi:10.1002/gepi.21648 PMID: 22674656
47. Hankinson JL, Crapo RO, Jensen RL. Spirometric reference values for the 6-s FVC maneuver. Chest. 2003;124(5):1805-11. Epub 2003/11/08. PMID: 14605052
48. Hankinson JL, Kawut SM, Shahar E, Smith LJ, Stukovsky KH, Barr RG. Performance of American Thoracic Society-recommended spirometry reference values in a multiethnic sample of adults: the multiethnic study of atherosclerosis (MESA) lung study. Chest. 2010;137(1):138-45. Epub 2009/09/11. doi:10.1378/chest.09-0919 PMID: 19741060
49. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841-2. doi:10.1093/bioinformatics/btq033 PMID: 20110278
50. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, et al. The UCSC Table Browser data retrieval tool. Nucleic acids research. 2004;32(Database issue):D493-6. Epub 2003/12/19. doi:10.1093/nar/gkh103 PMID: 14681465
51. Lawrence R, Day-Williams AG, Elliott KS, Morris AP, Zeggini E. CCRaVAT and QuTie-enabling analysis of rare variants in large-scale case control and quantitative trait association studies. BMC bioinformatics. 2010;11:527. Epub 2010/10/23. doi:10.1186/1471-2105-11-527 PMID: 20964851
52. Li J, Ji L. Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix. Heredity. 2005;95(3):221-7. Epub 2005/08/04. doi:10.1038/sj.hdy.6800717 PMID: 16077740
53. Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 2009;5(6):e1000529. Epub 2009/06/23. doi:10.1371/journal.pgen. 1000529 PMID: 19543373