A genome-wide association study in hispanics/latinos identifies novel signals for lung function the hispanic community health study/study of latinos

American Journal of Respiratory and Critical Care Medicine

Volumn 198, Issue 2, 2018, Pages 208-219

  Burkart, Kristin M ^a   Sofer, Tamar ^b,c   London, Stephanie J ^d   Manichaikul, Ani ^e   Hartwig, Fernando P ^f   Yan, Qi ^g   Artigas, María Soler ^h   Avila, Lydiana ⁱ   Chen, Wei ^g   Thomas, Sonia Davis ^j   Diaz, Alejandro A ^b   Hall, Ian P ^k   Horta, Bernardo L ^f   Kaplan, Robert C ^l   Laurie, Cathy C ^c   Menezes, Ana M ^f   Morrison, Jean V ^m   Oelsner, Elizabeth C ^a   Rastogi, Deepa ^l   Rich, Stephen S ^e   Soto Quiros, Manuel ^g   Stilp, Adrienne M ^c   Tobin, Martin D ^h,n   Wain, Louise V ^h,n   Celedón, Juan C ^g   Graham Barr, R ^a,o   more..

^a Columbia University Medical Center ^*  (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

^d NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^e UNIVERSITY OF VIRGINIA   (United States)

^f FEDERAL UNIVERSITY OF PELOTAS   (Brazil)

^g CHILDREN S HOSPITAL OF PITTSBURGH   (United States)

^h UNIVERSITY OF LEICESTER   (United Kingdom)

ⁱ HOSPITAL NACIONAL DE NIÑOS   (Costa Rica)

^j University of North Carolina at Chapel Hill   (United States)

^k UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^l ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^m UNIVERSITY OF CHICAGO   (United States)

ⁿ GLENFIELD HOSPITAL   (United Kingdom)

^o Department of Medicine   (United States)

more..

Author keywords

Chronic bstructive pulmonary disease; Genome wide association study; Hispanic Latino; Ingle nucleotide polymorphisms; Lung function

Indexed keywords

ADULT; AFRICAN; AGMO GENE; AMERICAN INDIAN; ARTICLE; CENTRAL AMERICAN; CHRONIC OBSTRUCTIVE LUNG DISEASE; COHORT ANALYSIS; CONTROLLED STUDY; CUBAN; DOMINICAN (DOMINICA); FEMALE; FORCED EXPIRATORY VOLUME; FORCED VITAL CAPACITY; GENE; GENE FREQUENCY; GENE LOCUS; GENE MAPPING; GENOME-WIDE ASSOCIATION STUDY; HAL GENE; HUMAN; LUNG FUNCTION; MAJOR CLINICAL STUDY; MALE; MEXICAN; MIDDLE AGED; PHENOTYPE; PRIORITY JOURNAL; PUERTO RICAN; REPLICATION STUDY; SINGLE NUCLEOTIDE POLYMORPHISM; SMOKING; SOUTH AMERICAN; ZSWIM7 GENE; ADOLESCENT; AGED; CAUCASIAN; COMPARATIVE STUDY; EUROPE; GENETIC PREDISPOSITION; GENETICS; HISPANIC; LUNG FUNCTION TEST; UNITED STATES; YOUNG ADULT;

ADOLESCENT; ADULT; AGED; COHORT STUDIES; EUROPE; EUROPEAN CONTINENTAL ANCESTRY GROUP; FEMALE; GENE FREQUENCY; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HISPANIC AMERICANS; HUMANS; MALE; MIDDLE AGED; PULMONARY DISEASE, CHRONIC OBSTRUCTIVE; RESPIRATORY FUNCTION TESTS; UNITED STATES; YOUNG ADULT;

EID: 85050092827     PISSN: 1073449X     EISSN: 15354970     Source Type: Journal    
DOI: 10.1164/rccm.201707-1493OC     Document Type: Article

References (72)

1. U.S. Census Bureau. 2012 national population projections. Table 4. Projections of the population by sex, race, and Hispanic origin for the United States: 2015 to 2060. 2012 [accessed 2016 Oct 10]. Available from: https://www.census.gov/data/tables/2012/demo/popproj/2012summary-tables.html.
2. Brehm JM, Celedón JC. Chronic obstructive pulmonary disease in Hispanics. Am J Respir Crit Care Med 2008;177:473–478.
3. Hunninghake GM, Weiss ST, Celedón JC. Asthma in Hispanics. Am J Respir Crit Care Med 2006;173:143–163.
4. Bryc K, Velez C, Karafet T, Moreno-Estrada A, Reynolds A, Auton A, et al. Genome-wide patterns of population structure and admixture among Hispanic/Latino populations. Proc Natl Acad Sci USA 2010; 107:8954–8961.
5. Vestbo J, Hurd SS, Agustí AG, Jones PW, Vogelmeier C, Anzueto A, et al. Global strategy for the diagnosis, management, and prevention of chronic obstructive pulmonary disease: GOLD executive summary. Am J Respir Crit Care Med 2013;187:347–365.
6. Vogelmeier CF, Criner GJ, Martinez FJ, Anzueto A, Barnes PJ, Bourbeau J, et al. Global strategy for the diagnosis, management, and prevention of chronic obstructive lung disease 2017 report: GOLD executive summary. Am J Respir Crit Care Med 2017;195: 557–582.
7. Miniño AM, Xu J, Kochanek KD. Deaths: preliminary data for 2008. Natl Vital Stat Rep 2010;59:1–52.
8. Kosacz NM, Croxton TL, Kiley JP, Weinmann GG, Wheaton AG, Ford ES, et al. Chronic obstructive pulmonary disease among adults: United States, 2011. MMWR 2012;61:938–943.
9. Díaz AA, Celli B, Celedón JC. Chronic obstructive pulmonary disease in Hispanics: a 9-year update. Am J Respir Crit Care Med 2018;197: 15–21.
10. Barr RG, Avilés-Santa L, Davis SM, Aldrich TK, Gonzalez F, Henderson AG, et al. Pulmonary disease and age at immigration among Hispanics: results from the Hispanic Community Health Study/Study of Latinos. Am J Respir Crit Care Med 2015;193: 386–395.
11. Bruse S, Sood A, Petersen H, Liu Y, Leng S, Celedón JC, et al. New Mexican Hispanic smokers have lower odds of chronic obstructive pulmonary disease and less decline in lung function than non-Hispanic whites. Am J Respir Crit Care Med 2011;184:1254–1260.
12. Diaz AA, Come CE, Mannino DM, Pinto-Plata V, Divo MJ, Bigelow C, et al. Obstructive lung disease in Mexican Americans and non-Hispanic whites: an analysis of diagnosis and survival in the National Health and Nutritional Examination Survey III follow-up study. Chest 2014;145:282–289.
13. Chen W, Brehm JM, Manichaikul A, Cho MH, Boutaoui N, Yan Q, et al. A genome-wide association study of chronic obstructive pulmonary disease in Hispanics. Ann Am Thorac Soc 2015;12:340–348.
14. Burkart KM, Manichaikul A, Wilk JB, Ahmed FS, Burke GL, Enright P, et al. APOM and high-density lipoprotein cholesterol are associated with lung function and per cent emphysema. Eur Respir J 2014;43: 1003–1017.
15. Manichaikul A, Hoffman EA, Smolonska J, Gao W, Cho MH, Baumhauer H, et al. Genome-wide study of percent emphysema on computed tomography in the general population: the Multi-Ethnic Study of Atherosclerosis Lung/SNP Health Association Resource Study. Am J Respir Crit Care Med 2014; 189:408–418.
16. 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. Nat Genet 2011;43: 1082–1090.
17. 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. Nat Commun 2015;6: 8658.
18. Soler Artigas M, Wain LV, Repapi E, Obeidat ME, Sayers I, Burton PR, et al.; SpiroMeta Consortium. Effect of five genetic variants associated with lung function on the risk of chronic obstructive lung disease, and their joint effects on lung function. Am J Respir Crit Care Med 2011;184:786–795.
19. Hancock DB, Soler Artigas M, Gharib SA, Henry A, Manichaikul A, Ramasamy A, et al.Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. PLoS Genet 2012;8:e1003098.
20. Pillai SG. A genome-wide association study in chronic obstructive pulmonary disease (COPD): identification of two major susceptibility loci. PLoS Genet 2009;5:e1000421.
21. Wilk JB. A genome-wide association study of pulmonary function measures in the Framingham Heart Study. PLoS Genet 2009;5: e1000429.
22. Wilk JB, Shrine NRG, 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. Am J Respir Crit Care Med 2012;186:622–632.
23. Cho MH, Boutaoui N, Klanderman BJ, Sylvia JS, Ziniti JP, Hersh CP, et al. Variants in FAM13A are associated with chronic obstructive pulmonary disease. Nat Genet 2010;42:200–202.
24. Castaldi PJ, Cho MH, Litonjua AA, Bakke P, Gulsvik A, Lomas DA, et al.; COPDGene and Eclipse Investigators. The association of genome-wide significant spirometric loci with chronic obstructive pulmonary disease susceptibility. Am J Respir Cell Mol Biol 2011;45: 1147–1153.
25. Cho MH, McDonald M-LN, Zhou X, Mattheisen M, Castaldi PJ, Hersh CP, et al.;NETT Genetics, ICGN, ECLIPSE and COPDGene Investigators. Risk loci for chronic obstructive pulmonary disease: a genome-wide association study and meta-analysis. Lancet Respir Med 2014;2:214–225.
26. 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. Nat Genet 2010;42: 45–52.
27. 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. Nat Genet 2010;42:36–44.
28. Wain LV, Shrine N, Artigas MS, Erzurumluoglu AM, Noyvert B, Bossini-Castillo L, et al. Genome-wide association analyses for lung function and chronic obstructive pulmonary disease identify new loci and potential druggable targets. Nat Genet 2017;49:416–425.
29. Hobbs BD, de Jong K, Lamontagne M, Bosse Y, Shrine N, Artigas MS, et al.; COPDGene Investigators; ECLIPSE Investigators, LifeLines Investigators, SPIROMICS Research Group, International COPD Genetics Network Investigators, UK BiLEVE Investigators, International COPD Genetics Consortium. Genetic loci associated with chronic obstructive pulmonary disease overlap with loci for lung function and pulmonary fibrosis. Nat Genet 2017;49:426–432.
30. LaVange LM, Kalsbeek WD, Sorlie PD, Avilés-Santa LM, Kaplan RC, Barnhart J, et al. Sample design and cohort selection in the Hispanic Community Health Study/Study of Latinos. Ann Epidemiol 2010;20: 642–649.
31. Burkart KM, Stilp AM, Sofer T, London SJ, Davis ST, Celedon JC, et al. Genome-wide association study (GWAS) of lung function among Hispanic/Latino individuals of diverse backgrounds. The Hispanic Community Health Study/Study of Latinos [abstract]. Am J Respir Crit Care Med 2015;191:A1069.
32. Sorlie PD, Avilés-Santa LM, Wassertheil-Smoller S, Kaplan RC, Daviglus ML, Giachello AL, et al. Design and implementation of the Hispanic Community Health Study/Study of Latinos. Ann Epidemiol 2010;20:629–641.
33. Conomos MP, Laurie CA, Stilp AM, Gogarten SM, McHugh CP, Nelson SC, et al. Genetic diversity and association studies in us hispanic/latino populations: applications in the Hispanic Community Health Study/Study of Latinos. Am J Hum Genet 2016; 98:165–184.
34. Pellegrino R. Interpretative strategies for lung function tests. Eur Respir J 2005;26:948–968.
35. Hankinson JL, Odencrantz JR, Fedan KB. Spirometric reference values from a sample of the general U.S. population. Am J Respir Crit Care Med 1999;159:179–187.
36. LaVange L, Davis SM, Hankinson J, Enright P, Wilson MR, Barr RG, et al. Spirometry reference equations from HCHS/SOL (Hispanic Community Health Study/Study of Latinos). Am J Respir Crit Care Med 2017;196:993–1003.
37. Laurie CC, Doheny KF, Mirel DB, Pugh EW, Bierut LJ, Bhangale T, et al.;GENEVA Investigators. Quality control and quality assurance in genotypic data for genome-wide association studies. Genet Epidemiol 2010;34:591–602.
38. 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: 56–65.
39. Sofer T, Shaffer JR, Graff M, Qi Q, Stilp AM, Gogarten SM, et al. Meta-analysis of genome-wide association studies with correlated individuals: application to the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Genet Epidemiol 2016;40: 492–501.
40. Pe’er I, Yelensky R, Altshuler D, Daly MJ. Estimation of the multiple testing burden for genomewide association studies of nearly all common variants. Genet Epidemiol 2008;32:381–385.
41. Chen H, Wang C, Conomos Matthew P, Stilp Adrienne M, Li Z, Sofer T, et al. Control for population structure and relatedness for binary traits in genetic association studies via logistic mixed models. Am J Hum Genet 2016;98:653–666.
42. Browning SR, Grinde K, Plantinga A, Gogarten SM, Stilp AM, Kaplan RC, et al. Local ancestry inference in a large US-based Hispanic/Latino study: Hispanic Community Health Study/Study of Latinos (HCHS/SOL). G3 (Bethesda) 2016;6: 1525–1534.
43. Sofer T, Baier LJ, Browning SR, Thornton TA, Talavera GA, Wassertheil-Smoller S, et al. Admixture mapping in the Hispanic Community Health Study/Study of Latinos reveals regions of genetic associations with blood pressure traits. PLoS One 2017;12: e0188400.
44. Zhang QS, Browning BL, Browning SR. ASAFE: ancestry-specific allele frequency estimation. Bioinformatics 2016;32: 2227–2229.
45. Bild DE, Bluemke DA, Burke GL, Detrano R, Diez Roux AV, Folsom AR, et al. Multi-ethnic study of atherosclerosis: objectives and design. Am J Epidemiol 2002;156:871–881.
46. Kaufman JD, Adar SD, Allen RW, Barr RG, Budoff MJ, Burke GL, et al. Prospective study of particulate air pollution exposures, subclinical atherosclerosis, and clinical cardiovascular disease: the Multi-Ethnic Study of Atherosclerosis and Air Pollution (MESA Air). Am J Epidemiol 2012;176:825–837.
47. Victora CG, Barros FC. Cohort profile: the 1982 Pelotas (Brazil) birth cohort study. Int J Epidemiol 2006;35:237–242.
48. Horta BL, Gigante DP, Gonçalves H, dos Santos Motta J, Loret de Mola C, Oliveira IO, et al. Cohort profile update: the 1982 Pelotas (Brazil) birth cohort study. Int J Epidemiol 2015;44: 441a–441e.
49. Chen W, Brehm JM, Boutaoui N, Soto-Quiros M, Avila L, Celli BR, et al. Native American ancestry, lung function, and COPD in Costa Ricans. Chest 2014;145:704–710.
50. Sofer T, Heller R, Bogomolov M, Avery CL, Graff M, North KE, et al. A powerful statistical framework for generalization testing in GWAS, with application to the HCHS/SOL. Genet Epidemiol 2017;41: 251–258.
51. Spier I, Kerick M, Drichel D, Horpaopan S, Altmüller J, Laner A, et al. Exome sequencing identifies potential novel candidate genes in patients with unexplained colorectal adenomatous polyposis. Fam Cancer 2016;15:281–288.
52. Sung YJ, de las Fuentes L, Schwander KL, Simino J, Rao DC. Gene–smoking interactions identify several novel blood pressure loci in the Framingham Heart Study. Am J Hypertens 2015;28: 343–354.
53. Martín V, Chahwan C, Gao H, Blais V, Wohlschlegel J, Yates JR, et al. Sws1 is a conserved regulator of homologous recombination in eukaryotic cells. EMBO J 2006;25:2564–2574.
54. Godin SK, Meslin C, Kabbinavar F, Bratton-Palmer DS, Hornack C, Mihalevic MJ, et al. Evolutionary and functional analysis of the invariant SWIM domain in the conserved Shu2/Sws1 protein family from Saccharomyces cerevisiae to Homo sapiens. Genetics 2015; 199:1023–1033.
55. Lou Z, Chen J. Cellular senescence and DNA repair. Exp Cell Res 2006; 312:2641–2646.
56. Tuder RM, Petrache I. Pathogenesis of chronic obstructive pulmonary disease. J Clin Invest 2012;122:2749–2755.
57. MacNee W, Tuder RM. New paradigms in the pathogenesis of chronic obstructive pulmonary disease I. Proc Am Thorac Soc 2009;6: 527–531.
58. Neofytou E, Tzortzaki EG, Chatziantoniou A, Siafakas NM. DNA damage due to oxidative stress in chronic obstructive pulmonary disease (COPD). Int J Mol Sci 2012;13:16853–16864.
59. Caramori G, Adcock IM, Casolari P, Ito K, Jazrawi E, Tsaprouni L, et al. Unbalanced oxidant-induced DNA damage and repair in COPD: a link towards lung cancer. Thorax 2011;66:521–527.
60. Aoshiba K, Zhou F, Tsuji T, Nagai A. DNA damage as a molecular link in the pathogenesis of COPD in smokers. Eur Respir J 2012;39: 1368.
61. National Center for Biotechnology Information. dbSNP: Rs192375903; build 38 [accessed 2016 Nov 1]. Available from: https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=192375903.
62. Suchi M, Sano H, Mizuno H, Wada Y. Molecular cloning and structural characterization of the human histidase gene (HAL). Genomics 1995; 29:98–104.
63. Yu B, Li AH, Muzny D, Veeraraghavan N, de Vries PS, Bis JC, et al. Association of rare loss-of-function alleles in HAL, serum histidine levels and incident coronary heart disease. Circ Cardiovasc Genet 2015;8:351–355.
64. Taylor RG, Lambert MA, Sexsmith E, Sadler SJ, Ray PN, Mahuran DJ, et al. Cloning and expression of rat histidase: homology to two bacterial histidases and four phenylalanine ammonia-lyases. J Biol Chem 1990;265:18192–18199.
65. Niu Y-C, Feng R-N, Hou Y, Li K, Kang Z, Wang J, et al. Histidine and arginine are associated with inflammation and oxidative stress in obese women. Br J Nutr 2012;108:57–61.
66. Watanabe M, Suliman ME, Qureshi AR, Garcia-Lopez E, Barany P, Heimburger O, et al. Consequences of low plasma histidine in chronic kidney disease patients: associations with inflammation, oxidative stress, and mortality. Am J Clin Nutr 2008;87:1860–1866.
67. Ubhi BK, Cheng KK, Dong J, Janowitz T, Jodrell D, Tal-Singer R, et al. Targeted metabolomics identifies perturbations in amino acid metabolism that sub-classify patients with copd. Mol Biosyst 2012;8:3125–3133.
68. Wyss AB, Sofer T, Lee MK, Terzikhan N, Nguyen JN, Lahousse L, et al. Multiethnic meta-analysis identifies new loci for pulmonary function. bioRxiv [online ahead of print] 5 Oct 2017; DOI: https://doi.org/10.1101/196048.
69. National Center for Biotechnology Information. dbSNP: Rs7228593; build 38 [accessed 2016 Nov]. Available from: https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=7228593.
70. Pouladi N, Bime C, Garcia JGN, Lussier YA. Complex genetics of pulmonary diseases: lessons from genome-wide association studies and next-generation sequencing. Transl Res 2016;168: 22–39.
71. Loth DW, Artigas MS, Gharib SA, Wain LV, Franceschini N, Koch B, et al. Genome-wide association analysis identifies six new loci associated with forced vital capacity. Nat Genet 2014;46: 669–677.
72. 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. Lancet Respir Med 2015;3:769–781. [Published erratum appears in Lancet Respir Med 4:e4.]