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Review

Using Epigenome-Wide Association Scans of DNA Methylation in Age-Related Complex Human Traits

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Pages 511-526 | Published online: 06 Nov 2012

References

  • Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature447(7145) , 661–678 (2007).
  • Schones DE , ZhaoK. Genome-wide approaches to studying chromatin modifications. Nat. Rev. Genet.9(3) , 179–191 (2008).
  • Javierre BM , FernandezAF, RichterJet al. Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. Genome Res. 20(2) , 170–179 (2010).
  • Kaminsky Z , PetronisA, WangSCet al. Epigenetics of personality traits: an illustrative study of identical twins discordant for risk-taking behavior. Twin Res. Hum. Genet. 11(1) , 1–11 (2008).
  • Dempster EL , PidsleyR, SchalkwykLCet al. Disease-associated epigenetic changes in monozygotic twins discordant for schizophrenia and bipolar disorder. Hum. Mol. Genet. 20(24) , 4786–4796 (2011).
  • Gervin K , VigelandMD, MattingsdalMet al. DNA methylation and gene expression changes in monozygotic twins discordant for psoriasis: identification of epigenetically dysregulated genes. PLoS Genet. 8(1) , e1002454 (2012).
  • Rakyan VK , BeyanH, DownTAet al. Identification of Type 1 diabetes-associated DNA methylation variable positions that precede disease diagnosis. PLoS Genet. 7(9) , e1002300 (2011).
  • Bell CG , TeschendorffAE, RakyanVK, MaxwellAP, BeckS, SavageDA. Genome-wide DNA methylation analysis for diabetic nephropathy in Type 1 diabetes mellitus. BMC Med. Genomics3 , 33 (2010).
  • Chowdhury S , ClevesMA, MacleodSL, JamesSJ, ZhaoW, HobbsCA. Maternal DNA hypomethylation and congenital heart defects. Birth Defects Res. A Clin. Mol. Teratol.91(2) , 69–76 (2011).
  • Breitling LP , YangR, KornB, BurwinkelB, BrennerH. Tobacco-smoking-related differential DNA methylation: 27K discovery and replication. Am. J. Hum. Genet.88(4) , 450–457 (2011).
  • Toperoff G , AranD, KarkJDet al. Genome-wide survey reveals predisposing diabetes Type 2-related DNA methylation variations in human peripheral blood. Hum. Mol. Genet. 21(2) , 371–383 (2012).
  • Bakulski KM , DolinoyDC, SartorMAet al. Genome-wide DNA methylation differences between late-onset Alzheimer‘s disease and cognitively normal controls in human frontal cortex. J. Alzheimer‘s Dis. 29(3) , 571–588 (2012).
  • Cheung HH , LeeTL, DavisAJ, TaftDH, RennertOM, ChanWY. Genome-wide DNA methylation profiling reveals novel epigenetically regulated genes and non-coding RNAs in human testicular cancer. Br. J. Cancer102(2) , 419–427 (2010).
  • Michaelson-Cohen R , KeshetI, StraussmanR, HechtM, CedarH, BellerU. Genome-wide de novo methylation in epithelial ovarian cancer. Int. J. Gynecol. Cancer21(2) , 269–279 (2011).
  • Kim JH , DhanasekaranSM, PrensnerJRet al. Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. Genome Res. 21(7) , 1028–1041 (2011).
  • Rakyan VK , DownTA, BaldingDJ, BeckS. Epigenome-wide association studies for common human diseases. Nat. Rev. Genet.12(8) , 529–541 (2011).
  • Heijmans BT , MillJ. Commentary: the seven plagues of epigenetic epidemiology. Int. J. Epidemiol.41(1) , 74–78 (2012).
  • Doi A , ParkIH, WenBet al. Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat. Genet. 41(12) , 1350–1353 (2009).
  • Cedar H , BergmanY. Linking DNA methylation and histone modification: patterns and paradigms. Nat. Rev. Genet.10(5) , 295–304 (2009).
  • Bell JT , PaiAA, PickrellJKet al. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol. 12(1) , R10 (2011).
  • Lister R , PelizzolaM, DowenRHet al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462(7271) , 315–322 (2009).
  • Reik W . Stability and flexibility of epigenetic gene regulation in mammalian development. Nature447(7143) , 425–432 (2007).
  • Feinberg AP . Phenotypic plasticity and the epigenetics of human disease. Nature447(7143) , 433–440 (2007).
  • Eckhardt F , LewinJ, CorteseRet al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat. Genet. 38(12) , 1378–1385 (2006).
  • Aran D , ToperoffG, RosenbergM, HellmanA. Replication timing-related and gene body-specific methylation of active human genes. Hum. Mol. Genet.20(4) , 670–680 (2011).
  • Jjingo D , ConleyAB, YiSV, LunyakVV, JordanIK. On the presence and role of human gene-body DNA methylation. Oncotarget3(4) , 462–474 (2012).
  • Ramsahoye BH , BiniszkiewiczD, LykoF, ClarkV, BirdAP, JaenischR. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc. Natl Acad. Sci. USA97(10) , 5237–5242 (2000).
  • Bell JT , TsaiPC, YangTPet al. Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population. PLoS Genet. 8(4) , e1002629 (2012).
  • Christensen BC , HousemanEA, MarsitCJet al. Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. PLoS Genet. 5(8) , e1000602 (2009).
  • Gronniger E , WeberB, HeilOet al. Aging and chronic sun exposure cause distinct epigenetic changes in human skin. PLoS Genet. 6(5) , e1000971 (2010).
  • Bjornsson HT , SigurdssonMI, FallinMDet al. Intra-individual change over time in DNA methylation with familial clustering. JAMA 299(24) , 2877–2883 (2008).
  • Fraga MF , BallestarE, PazMFet al. Epigenetic differences arise during the lifetime of monozygotic twins. Proc. Natl Acad. Sci. USA 102(30) , 10604–10609 (2005).
  • Kaminsky ZA , TangT, WangSCet al. DNA methylation profiles in monozygotic and dizygotic twins. Nat. Genet. 41(2) , 240–245 (2009).
  • Gibbs JR , Van Der Brug MP, Hernandez DG et al. Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet.6(5) , e1000952 (2010).
  • Gamazon ER , BadnerJA, ChengLet al. Enrichment of cis-regulatory gene expression SNPs and methylation quantitative trait loci among bipolar disorder susceptibility variants. Mol. Psychiat. doi:10.1038/mp.2011.174 (2012) (Epub ahead of print).
  • Numata S , YeT, HydeTMet al. DNA methylation signatures in development and aging of the human prefrontal cortex. Am. J. Hum. Genet. 90(2) , 260–272 (2012).
  • Gertz J , VarleyKE, ReddyTEet al. Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet. 7(8) , e1002228 (2011).
  • Schilling E , El Chartouni C, Rehli M. Allele-specific DNA methylation in mouse strains is mainly determined by cis-acting sequences. Genome Res.19(11) , 2028–2035 (2009).
  • Rakyan VK , DownTA, ThorneNPet al. An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res. 18(9) , 1518–1529 (2008).
  • Thompson RF , AtzmonG, GheorgheCet al. Tissue-specific dysregulation of DNA methylation in aging. Aging Cell 9(4) , 506–518 (2010).
  • Heijmans BT , TobiEW, LumeyLH, SlagboomPE. The epigenome: archive of the prenatal environment. Epigenetics4(8) , 526–531 (2009).
  • Ollikainen M , SmithKR, JooEJet al. DNA methylation analysis of multiple tissues from newborn twins reveals both genetic and intrauterine components to variation in the human neonatal epigenome. Hum. Mol. Genet. 19(21) , 4176–4188 (2010).
  • Wong CC , CaspiA, WilliamsBet al. A longitudinal study of epigenetic variation in twins. Epigenetics 5(6) , 516–526 (2010).
  • Bell JT , SpectorTD. A twin approach to unraveling epigenetics. Trends Genet.27(3) , 116–125 (2011).
  • Laird PW . Principles and challenges of genomewide DNA methylation analysis. Nat. Rev. Genet.11(3) , 191–203 (2010).
  • Bibikova M , LeJ, BarnesBet al. Genome-wide DNA methylation profiling using Infinium® assay. Epigenomics 1(1) , 177–200 (2009).
  • Dedeurwaerder S , DefranceM, CalonneE, DenisH, SotiriouC, FuksF. Evaluation of the infinium methylation 450K technology. Epigenomics3(6) , 771–784 (2011).
  • Irizarry RA , Ladd-AcostaC, CarvalhoBet al. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res. 18(5) , 780–790 (2008).
  • Down TA , RakyanVK, TurnerDJet al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat. Biotechnol. 26(7) , 779–785 (2008).
  • Huang Y , PastorWA, ShenY, TahilianiM, LiuDR, RaoA. The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS ONE5(1) , e8888 (2010).
  • Sandoval J , HeynH, MoranSet al. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics 6(6) , 692–702 (2011).
  • Gervin K , HammeroM, AkselsenHEet al. Extensive variation and low heritability of DNA methylation identified in a twin study. Genome Res. 21(11) , 1813–1821 (2011).
  • Meissner A , GnirkeA, BellGW, RamsahoyeB, LanderES, JaenischR. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res.33(18) , 5868–5877 (2005).
  • Leek JT , StoreyJD. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet.3(9) , 1724–1735 (2007).
  • Leek JT , ScharpfRB, BravoHCet al. Tackling the widespread and critical impact of batch effects in high-throughput data. Nat. Rev. Genet. 11(10) , 733–739 (2010).
  • Du P , ZhangX, HuangCCet al. Comparison of β-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics 11 , 587 (2010).
  • Bell JT , SafferyR. The value of twins in epigenetic epidemiology. Int. J. Epidemiol.41(1) , 140–150 (2012).
  • Bulmer MG . The Bology of Twinning in Man. Clarendon Press, Oxford, UK (1970).
  • Wang S . Method to detect differentially methylated loci with case–control designs using Illumina arrays. Genet. Epidemiol.35(7) , 686–694 (2011).
  • Deveale B , Van Der Kooy D, Babak T. Critical evaluation of imprinted gene expression by RNA-seq: a new perspective. PLoS Genet.8(3) , e1002600 (2012).
  • Kelsey G , BartolomeiMS. Imprinted genes … and the number is? PLoS Genet.8(3) , e1002601 (2012).
  • Kleinman CL , MajewskiJ. Comment on “widespread RNA and DNA sequence differences in the human transcriptome”. Science335(6074) , 1302; author reply 1302 (2012).
  • Pickrell JK , GiladY, PritchardJK. Comment on “widespread RNA and DNA sequence differences in the human transcriptome”. Science335(6074) , 1302; author reply 1302 (2012).
  • Lin W , PiskolR, TanMH, LiJB. Comment on “widespread RNA and DNA sequence differences in the human transcriptome”. Science335(6074) , 1302; author reply 1302 (2012).
  • Hansen KD , TimpW, BravoHCet al. Increased methylation variation in epigenetic domains across cancer types. Nat. Genet. 43(8) , 768–775 (2011).
  • Berman BP , WeisenbergerDJ, AmanJFet al. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat. Genet. 44(1) , 40–46 (2012).
  • Mill J , TangT, KaminskyZet al. Epigenomic profiling reveals DNA-methylation changes associated with major psychosis. Am. J. Hum. Genet. 82(3) , 696–711 (2008).
  • Weksberg R , ShumanC, CaluseriuOet al. Discordant KCNQ1OT1 imprinting in sets of monozygotic twins discordant for Beckwith–Wiedemann syndrome. Hum. Mol. Genet. 11(11) , 1317–1325 (2002).
  • Handel AE , EbersGC, RamagopalanSV. Epigenetics: molecular mechanisms and implications for disease. Trends Mol. Med.16(1) , 7–16 (2010).
  • Handunnetthi L , HandelAE, RamagopalanSV. Contribution of genetic, epigenetic and transcriptomic differences to twin discordance in multiple sclerosis. Expert Rev. Neurother.10(9) , 1379–1381 (2010).
  • Marsit CJ , KoestlerDC, ChristensenBC, KaragasMR, HousemanEA, KelseyKT. DNA methylation array analysis identifies profiles of blood-derived DNA methylation associated with bladder cancer. J. Clin. Oncol.29(9) , 1133–1139 (2011).
  • Poulsen P , EstellerM, VaagA, FragaMF. The epigenetic basis of twin discordance in age-related diseases. Pediatr. Res.61(5 Pt 2) , R38–R42 (2007).
  • Ballestar E . Epigenetics lessons from twins: prospects for autoimmune disease. Clin. Rev. Allergy Immunol.39(1) , 30–41 (2010).
  • Spector TD , CicuttiniF, BakerJ, LoughlinJ, HartD. Genetic influences on osteoarthritis in women: a twin study. BMJ312(7036) , 940–943 (1996).
  • Macgregor AJ , SniederH, RigbyASet al. Characterizing the quantitative genetic contribution to rheumatoid arthritis using data from twins. Arthritis Rheum. 43(1) , 30–37 (2000).
  • Arnett FC , ReveilleJD. Genetics of systemic lupus erythematosus. Rheum. Dis Clin. N. Am.18(4) , 865–892 (1992).
  • Baranzini SE , MudgeJ, van Velkinburgh JC et al. Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature464(7293) , 1351–1356 (2010).
  • Kerkel K , SpadolaA, YuanEet al. Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation. Nat. Genet. 40(7) , 904–908 (2008).
  • Schalkwyk LC , MeaburnEL, SmithRet al. Allelic skewing of DNA methylation is widespread across the genome. Am. J. Hum. Genet. 86(2) , 196–212 (2010).
  • Wong CCY , SchalkwykLC, MeaburnELet al. Genome-wide DNA methylation profiling of monozygotic twins discordant for autism spectrum disorder. Presented at: 12th International Congress of Human Genetics/61st Annual Meeting of the American Society of Human Genetics. Montreal, Canada, 11–15 October 2011 (Abstract 25).
  • Kobayashi Y , AbsherDM, GulzarZGet al. DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer. Genome Res. 21(7) , 1017–1027 (2011).
  • Fackler MJ , UmbrichtCB, WilliamsDet al. Genome-wide methylation analysis identifies genes specific to breast cancer hormone receptor status and risk of recurrence. Cancer Res. 71(19) , 6195–6207 (2011).
  • Feinberg AP , TyckoB. The history of cancer epigenetics. Nat. Rev. Cancer4(2) , 143–153 (2004).
  • Madrigano J , BaccarelliA, MittlemanMAet al. Aging and epigenetics: longitudinal changes in gene-specific DNA methylation. Epigenetics 7(1) (2012).
  • Talens RP , BoomsmaDI, TobiEWet al. Variation, patterns, and temporal stability of DNA methylation: considerations for epigenetic epidemiology. FASEB J. 24(9) , 3135–3144 (2010).
  • Heyn H , LiN, FerreiraHJet al. Distinct DNA methylomes of newborns and centenarians. Proc. Natl Acad. Sci. USA (2012).
  • Bollati V , SchwartzJ, WrightRet al. Decline in genomic DNA methylation through aging in a cohort of elderly subjects. Mechanisms Ageing Dev. 130(4) , 234–239 (2009).
  • Boks MP , DerksEM, WeisenbergerDJet al. The relationship of DNA methylation with age, gender and genotype in twins and healthy controls. PLoS ONE 4(8) , e6767 (2009).
  • Fernandez AF , AssenovY, Martin-SuberoJIet al. A DNA methylation fingerprint of 1628 human samples. Genome Res. 22(2) , 407–419 (2012).
  • Teschendorff AE , MenonU, Gentry-MaharajAet al. Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res. 20(4) , 440–446 (2010).
  • Rakyan VK , DownTA, MaslauSet al. Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res. 20(4) , 434–439 (2010).
  • Hernandez DG , NallsMA, GibbsJRet al. Distinct DNA methylation changes highly correlated with chronological age in the human brain. Hum. Mol. Genet. 20(6) , 1164–1172 (2011).
  • Bocklandt S , LinW, SehlMEet al. Epigenetic predictor of age. PLoS ONE 6(6) , e14821 (2011).
  • Koch CM , WagnerW. Epigenetic-aging-signature to determine age in different tissues. Aging3(10) , 1018–1027 (2011).
  • Adkins RM , ThomasF, TylavskyFA, KrushkalJ. Parental ages and levels of DNA methylation in the newborn are correlated. BMC Med. Genet.12 , 47 (2011).
  • Alisch RS , BarwickBG, ChopraPet al. Age-associated DNA methylation in pediatric populations. Genome Res. 22(4) , 623–632 (2012).
  • Koch CM , SuschekCV, LinQet al. Specific age-associated DNA methylation changes in human dermal fibroblasts. PLoS ONE 6(2) , e16679 (2011).
  • Berdasco M , EstellerM. Hot topics in epigenetic mechanisms of aging: 2011. Aging Cell11(2) , 181–186 (2012).
  • Liu L , RandoTA. Manifestations and mechanisms of stem cell aging. J. Cell Biol.193(2) , 257–266 (2011).
  • Rodrigues AA Jr, Suaid HJ, Fazan VP et al. Histologic study of urethral extracellular matrix and collagen from aging and long-term alloxan-induced diabetic male rats. Urology77(2) , 510.e6–e11 (2011).
  • Bell CG , FinerS, LindgrenCMet al. Integrated genetic and epigenetic analysis identifies haplotype-specific methylation in the FTO Type 2 diabetes and obesity susceptibility locus. PLoS ONE 5(11) , e14040 (2010).
  • Slatkin M . Epigenetic inheritance and the missing heritability problem. Genetics182(3) , 845–850 (2009).

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