Differences in smoking associated DNA methylation patterns in South Asians and Europeans
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Lim SS, Vos T, Flaxman AD, Danaei G, Shibuya K, Adair-Rohani H, Amann M, Anderson HR, Andrews KG, Aryee M, Atkinson C, Bacchus LJ, Bahalim AN, Balakrishnan K, Balmes J, Barker-Collo S, Baxter A, Bell ML, Blore JD, Blyth F, Bonner C, Borges G, Bourne R, Boussinesq M, Brauer M, Brooks P, Bruce NG, Brunekreef B, Bryan-Hancock C, Bucello C: A comparative risk assessment of burden of disease and injury attributable to 67 risk factors and risk factor clusters in 21 regions, 1990–2010: a systematic analysis for the global burden of disease study 2010. Lancet. 2012, 380: 2224-2260. 10.1016/S0140-6736(12)61766-8.
Breitling LP, Yang R, Korn B, Burwinkel B, Brenner H: Tobacco-smoking-related differential DNA methylation: 27K discovery and replication. Am J Hum Genet. 2011, 88: 450-457. 10.1016/j.ajhg.2011.03.003.
Wan ES, Qiu W, Baccarelli A, Carey VJ, Bacherman H, Rennard SI, Agusti A, Anderson W, Lomas DA, Demeo DL: Cigarette smoking behaviors and time since quitting are associated with differential DNA methylation across the human genome. Hum Mol Genet. 2012, 21: 3073-3082. 10.1093/hmg/dds135.
Joubert BR, Haberg SE, Nilsen RM, Wang X, Vollset SE, Murphy SK, Huang Z, Hoyo C, Midttun O, Cupul-Uicab LA, Ueland PM, Wu MC, Nystad W, Bell DA, Peddada SD, London SJ: 450K epigenome-wide scan identifies differential DNA methylation in newborns related to maternal smoking during pregnancy. Environ Health Perspect. 2012, 120: 1425-1431. 10.1289/ehp.1205412.
Philibert RA, Beach SR, Brody GH: Demethylation of the aryl hydrocarbon receptor repressor as a biomarker for nascent smokers. Epigenetics. 2012, 7: 1331-1338. 10.4161/epi.22520.
Shenker NS, Polidoro S, van Veldhoven K, Sacerdote C, Ricceri F, Birrell MA, Belvisi MG, Brown R, Vineis P, Flanagan JM: Epigenome-wide association study in the European prospective investigation into cancer and nutrition (EPIC-Turin) identifies novel genetic loci associated with smoking. Hum Mol Genet. 2013, 22: 843-851. 10.1093/hmg/dds488.
Zeilinger S, Kuhnel B, Klopp N, Baurecht H, Kleinschmidt A, Gieger C, Weidinger S, Lattka E, Adamski J, Peters A, Strauch K, Waldenberger M, Illig T: Tobacco smoking leads to extensive genome-wide changes in DNA methylation. PLoS One. 2013, 8: e63812-10.1371/journal.pone.0063812.
Shenker NS, Ueland PM, Polidoro S, van Veldhoven K, Ricceri F, Brown R, Flanagan JM, Vineis P: DNA methylation as a long-term biomarker of exposure to tobacco smoke. Epidemiology. 2013, 24: 712-716. 10.1097/EDE.0b013e31829d5cb3.
Chavan H, Krishnamurthy P: Polycyclic aromatic hydrocarbons (PAHs) mediate transcriptional activation of the ATP binding cassette transporter ABCB6 gene via the aryl hydrocarbon receptor (AhR). J Biol Chem. 2012, 287: 32054-32068. 10.1074/jbc.M112.371476.
Ge C, Ye J, Wang Q, Zhang C, Yang JM, Qian G: Polycyclic aromatic hydrocarbons suppress meiosis in primordial germ cells via the AHR signaling pathway. Toxicol Lett. 2012, 210: 285-292. 10.1016/j.toxlet.2012.02.014.
Breitling LP, Salzmann K, Rothenbacher D, Burwinkel B, Brenner H: Smoking, F2RL3 methylation, and prognosis in stable coronary heart disease. Eur Heart J. 2012, 33: 2841-2848. 10.1093/eurheartj/ehs091.
Jafar TH, Haaland BA, Rahman A, Razzak JA, Bilger M, Naghavi M, Mokdad AH, Hyder AA: Non-communicable diseases and injuries in Pakistan: strategic priorities. Lancet. 2013, 381: 2281-2290. 10.1016/S0140-6736(13)60646-7.
Elliott HR, Walia GK, Duggirala A, Groom A, Reddy SU, Chandak GR, Gupta V, Laakso M, Dekker JM, Walker M, Ebrahim S, Smith GD, Relton CL, The RISC Consortium: Migration and DNA methylation: a comparison of methylation patterns in type 2 diabetes susceptibility genes between Indians and Europeans. J Diabetes Res Clin Metabol. 2013, 2:
Fraser HB, Lam LL, Neumann SM, Kobor MS: Population-specificity of human DNA methylation. Genome Biol. 2012, 13: R8-10.1186/gb-2012-13-2-r8.
Spencer K, Cowans NJ: Accuracy of self-reported smoking status in first trimester aneuploidy screening. Prenat Diagn. 2013, 33: 245-250. 10.1002/pd.4053.
Dietz PM, Homa D, England LJ, Burley K, Tong VT, Dube SR, Bernert JT: Estimates of nondisclosure of cigarette smoking among pregnant and nonpregnant women of reproductive age in the United States. Am J Epidemiol. 2011, 173: 355-359. 10.1093/aje/kwq381.
Jensen EJ, Pedersen B, Frederiksen R, Dahl R: Prospective study on the effect of smoking and nicotine substitution on leucocyte blood counts and relation between blood leucocytes and lung function. Thorax. 1998, 53: 784-789. 10.1136/thx.53.9.784.
Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y, Pritchard JK: DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol. 2011, 12: R10-10.1186/gb-2011-12-1-r10.
Gibbs JR, van der Brug MP, Hernandez DG, Traynor BJ, Nalls MA, Lai SL, Arepalli S, Dillman A, Rafferty IP, Troncoso J, Johnson R, Zielke HR, Ferrucci L, Longo DL, Cookson MR, Singleton AB: Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet. 2010, 6: e1000952-10.1371/journal.pgen.1000952.
Tillin T, Forouhi NG, McKeigue PM, Chaturvedi N: Southall and Brent REvisited: cohort profile of SABRE, a UK population-based comparison of cardiovascular disease and diabetes in people of European, Indian Asian and African Caribbean origins. Int J Epidemiol. 2012, 41: 33-42. 10.1093/ije/dyq175.
Touleimat N, Tost J: Complete pipeline for infinium((R)) human methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation. Epigenomics. 2012, 4: 325-341. 10.2217/epi.12.21.
Du P, Zhang X, Huang CC, Jafari N, Kibbe WA, Hou L, Lin SM: Comparison of beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics. 2010, 11: 587-10.1186/1471-2105-11-587.
Houseman EA, Accomando WP, Koestler DC, Christensen BC, Marsit CJ, Nelson HH, Wiencke JK, Kelsey KT: DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics. 2012, 13: 86-10.1186/1471-2105-13-86.
Johnson WE, Li C, Rabinovic A: Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2007, 8: 118-127. 10.1093/biostatistics/kxj037.
Du P, Kibbe WA, Lin SM: lumi: a pipeline for processing Illumina microarray. Bioinformatics. 2008, 24: 1547-1548. 10.1093/bioinformatics/btn224.
Davis S, Du P, Bilke S, Triche T, Bootwalla M: methylumi: Handle Illumina methylation data. 2013, In R package 2.6.1. [ http://www.bioconductor.org/packages/2.14/bioc/html/methylumi.html ]
Barfield RT, Kilaru V, Smith AK, Conneely KN: CpGassoc: an R function for analysis of DNA methylation microarray data. Bioinformatics. 2012, 28: 1280-1281. 10.1093/bioinformatics/bts124.
Leek JT, Storey JD: A general framework for multiple testing dependence. Proc Natl Acad Sci U S A. 2008, 105: 18718-18723. 10.1073/pnas.0808709105.