Loos RJF. 15 years of genome-wide association studies and no signs of slowing down. Nat Commun. 2020;11(1):5900.
Article
CAS
Google Scholar
Tam V, Patel N, Turcotte M, Bosse Y, Pare G, Meyre D. Benefits and limitations of genome-wide association studies. Nat Rev Genet. 2019;20(8):467–84.
Article
CAS
Google Scholar
Mills MC, Rahal C. A scientometric review of genome-wide association studies. Commun Biol. 2019;2:9.
Article
Google Scholar
Waterland RA, Garza C. Potential mechanisms of metabolic imprinting that lead to chronic disease. Am.J.Clin.Nutr. 1999;69(2):179–97.
Article
CAS
Google Scholar
Waterland RA, Michels KB. Epigenetic epidemiology of the developmental origins hypothesis. Annu Rev Nutr. 2007;27:363–88.
Article
CAS
Google Scholar
Rakyan VK, Down TA, Balding DJ, Beck S. Epigenome-wide association studies for common human diseases. Nat Rev Genet. 2011;12(8):529–41.
Article
CAS
Google Scholar
Lappalainen T, Greally JM. Associating cellular epigenetic models with human phenotypes. Nat Rev Genet. 2017;18(7):441–51.
Article
CAS
Google Scholar
Roubroeks JAY, Smith AR, Smith RG, Pishva E, Ibrahim Z, Sattlecker M, et al. An epigenome-wide association study of Alzheimer’s disease blood highlights robust DNA hypermethylation in the HOXB6 gene. Neurobiol Aging. 2020;95:26–45.
Article
CAS
Google Scholar
Nabais MF, Laws SM, Lin T, Vallerga CL, Armstrong NJ, Blair IP, et al. Meta-analysis of genome-wide DNA methylation identifies shared associations across neurodegenerative disorders. Genome Biol. 2021;22(1):90.
Article
CAS
Google Scholar
van Dongen J, Bonder MJ, Dekkers KF, Nivard MG, van Iterson M, Willemsen G, et al. DNA methylation signatures of educational attainment. NPJ Sci Learn. 2018;3:7.
Article
Google Scholar
van Dongen J, Hagenbeek FA, Suderman M, Roetman PJ, Sugden K, Chiocchetti AG, et al. DNA methylation signatures of aggression and closely related constructs: a meta-analysis of epigenome-wide studies across the lifespan. Mol Psychiatry. 2021;26(6):2148–62.
Article
Google Scholar
Horvath S. DNA methylation age of human tissues and cell types. Genome Biol. 2013;14(10):R115.
Article
Google Scholar
Lu Y, Brommer B, Tian X, Krishnan A, Meer M, Wang C, et al. Reprogramming to recover youthful epigenetic information and restore vision. Nature. 2020;588(7836):124–9.
Article
CAS
Google Scholar
Chen BH, Marioni RE, Colicino E, Peters MJ, Ward-Caviness CK, Tsai PC, et al. DNA methylation-based measures of biological age: meta-analysis predicting time to death. Aging (Albany NY). 2016;8(9):1844–65.
Article
CAS
Google Scholar
Tsai PC, Glastonbury CA, Eliot MN, Bollepalli S, Yet I, Castillo-Fernandez JE, et al. Smoking induces coordinated DNA methylation and gene expression changes in adipose tissue with consequences for metabolic health. Clin Epigenetics. 2018;10(1):126.
Article
CAS
Google Scholar
Joubert BR, Felix JF, Yousefi P, Bakulski KM, Just AC, Breton C, et al. DNA methylation in newborns and maternal smoking in pregnancy: genome-wide consortium meta-analysis. Am J Hum Genet. 2016;98(4):680–96.
Article
CAS
Google Scholar
Carpenter BL, Remba TK, Thomas SL, Madaj Z, Brink L, Tiedemann RL, et al. Oocyte age and preconceptual alcohol use are highly correlated with epigenetic imprinting of a noncoding RNA (nc886). Proc Natl Acad Sci U S A. 2021;118(12):e2026580118.
Kupers LK, Monnereau C, Sharp GC, Yousefi P, Salas LA, Ghantous A, et al. Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight. Nat Commun. 2019;10(1):1893.
Article
Google Scholar
Wahl S, Drong A, Lehne B, Loh M, Scott WR, Kunze S, et al. Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity. Nature. 2017;541(7635):81–6.
Article
CAS
Google Scholar
Bjornsson HT, Sigurdsson MI, Fallin MD, Irizarry RA, Aspelund T, Cui H, et al. Intra-individual change over time in DNA methylation with familial clustering. JAMA. 2008;299(24):2877–83.
Article
CAS
Google Scholar
Zhang D, Cheng L, Badner JA, Chen C, Chen Q, Luo W, et al. Genetic control of individual differences in gene-specific methylation in human brain. Am J Hum Genet. 2010;86(3):411–9.
Article
CAS
Google Scholar
Villicana S, Bell JT. Genetic impacts on DNA methylation: research findings and future perspectives. Genome Biol. 2021;22(1):127.
Article
CAS
Google Scholar
Sanchez-Mut JV, Heyn H, Silva BA, Dixsaut L, Garcia-Esparcia P, Vidal E, et al. PM20D1 is a quantitative trait locus associated with Alzheimer’s disease. Nat Med. 2018;24(5):598–603.
Article
CAS
Google Scholar
Bonder MJ, Luijk R, Zhernakova DV, Moed M, Deelen P, Vermaat M, et al. Disease variants alter transcription factor levels and methylation of their binding sites. Nat Genet. 2017;49(1):131–8.
Article
CAS
Google Scholar
International HapMap, C. The international HapMap project. Nature. 2003;426(6968):789–96.
Article
Google Scholar
Genomes Project, C, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, et al. A global reference for human genetic variation. Nature. 2015;526(7571):68–74.
Article
Google Scholar
Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015;518(7539):317–30.
Article
CAS
Google Scholar
Martens JH, Stunnenberg HG. BLUEPRINT: mapping human blood cell epigenomes. Haematologica. 2013;98(10):1487–9.
Article
CAS
Google Scholar
Stunnenberg HG, Hirst M. The international human Epigenome Consortium: a blueprint for scientific collaboration and discovery. Cell. 2016;167(5):1145–9.
Article
CAS
Google Scholar
Wei S, Tao J, Xu J, Chen X, Wang Z, Zhang N, et al. Ten years of EWAS. Adv Sci (Weinh). 2021;8(20):e2100727.
Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, et al. High density DNA methylation array with single CpG site resolution. Genomics. 2011;98(4):288–95.
Article
CAS
Google Scholar
Pidsley R, Zotenko E, Peters TJ, Lawrence MG, Risbridger GP, Molloy P, et al. Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling. Genome Biol. 2016;17(1):208.
Article
Google Scholar
Bose M, Wu C, Pankow JS, Demerath EW, Bressler J, Fornage M, et al. Evaluation of microarray-based DNA methylation measurement using technical replicates: the atherosclerosis risk in communities (ARIC) study. BMC Bioinformatics. 2014;15:312.
Article
Google Scholar
Gallego-Pauls M, Hernandez-Ferrer C, Bustamante M, Basagana X, Barrera-Gomez J, Lau CE, et al. Variability of multi-omics profiles in a population-based child cohort. BMC Med. 2021;19(1):166.
Article
CAS
Google Scholar
Grundberg E, Meduri E, Sandling JK, Hedman AK, Keildson S, Buil A, et al. Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements. Am J Hum Genet. 2013;93(5):876–90.
Article
CAS
Google Scholar
Zaimi I, Pei D, Koestler DC, Marsit CJ, De Vivo I, Tworoger SS, et al. Variation in DNA methylation of human blood over a 1-year period using the Illumina MethylationEPIC array. Epigenetics. 2018;13(10-11):1056–71.
Article
Google Scholar
Gunasekara CJ, Scott CA, Laritsky E, Baker MS, MacKay H, Duryea JD, et al. A genomic atlas of systemic interindividual epigenetic variation in humans. Genome Biol. 2019;20(1):105.
Article
Google Scholar
Lonsdale J, Thomas J, Salvatore M, Phillips R, Lo E, et al. The genotype-tissue expression (GTEx) project. Nat Genet. 2013;45(6):580–5.
Article
CAS
Google Scholar
Hannon E, Lunnon K, Schalkwyk L, Mill J. Interindividual methylomic variation across blood, cortex, and cerebellum: implications for epigenetic studies of neurological and neuropsychiatric phenotypes. Epigenetics. 2015;10(11):1024–32.
Article
Google Scholar
Hannon E, Dempster E, Viana J, Burrage J, Smith AR, Macdonald R, et al. An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation. Genome Biol. 2016;17(1):176.
Article
Google Scholar
Rizzardi LF, Hickey PF, Idrizi A, Tryggvadóttir R, Callahan CM, Stephens KE, et al. Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits. Genome Biol. 2021;22(1):116.
Article
CAS
Google Scholar
Min JL, Hemani G, Hannon E, Dekkers KF, Castillo-Fernandez J, Luijk R, et al. Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation. Nat Genet. 2021;53(9):1311–21.
Article
CAS
Google Scholar
Busche S, Shao X, Caron M, Kwan T, Allum F, Cheung WA, et al. Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation. Genome Biol. 2015;16:290.
Article
Google Scholar
Luijk R, Goeman JJ, Slagboom EP, Heijmans BT, van Zwet EW. An alternative approach to multiple testing for methylation QTL mapping reduces the proportion of falsely identified CpGs. Bioinformatics. 2015;31(3):340–5.
Article
CAS
Google Scholar
Taylor DL, Jackson AU, Narisu N, Hemani G, Erdos MR, Chines PS, et al. Integrative analysis of gene expression, DNA methylation, physiological traits, and genetic variation in human skeletal muscle. Proc Natl Acad Sci U S A. 2019;116(22):10883–8.
Article
CAS
Google Scholar
Consortium, G.T., Laboratory, D.A., Coordinating Center -Analysis Working, G., Statistical Methods groups-Analysis Working, G., Enhancing, G.g., Fund, N.I.H.C., Nih/Nci, Nih/Nhgri, Nih/Nimh, Nih/Nida, et al. Genetic effects on gene expression across human tissues. Nature. 2017;550(7675):204–13.
Article
Google Scholar
Duhl DM, Vrieling H, Miller KA, Wolff GL, Barsh GS. Neomorphic agouti mutations in obese yellow mice. Nat.Genet. 1994;8(1):59–65.
Article
CAS
Google Scholar
Vasicek TJ, Zeng L, Guan XJ, Zhang T, Costantini F, Tilghman SM. Two dominant mutations in the mouse fused gene are the result of transposon insertions. Genetics. 1997;147(2):777–86.
Article
CAS
Google Scholar
Chuong EB, Elde NC, Feschotte C. Regulatory activities of transposable elements: from conflicts to benefits. Nat Rev Genet. 2017;18(2):71–86.
Article
CAS
Google Scholar
Gerdes P, Richardson SR, Mager DL, Faulkner GJ. Transposable elements in the mammalian embryo: pioneers surviving through stealth and service. Genome Biol. 2016;17:100.
Article
Google Scholar
Khan H, Smit A, Boissinot S. Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res. 2006;16(1):78–87.
Article
CAS
Google Scholar
Morrow JD, Glass K, Cho MH, Hersh CP, Pinto-Plata V, Celli B, et al. Human lung DNA methylation quantitative trait loci colocalize with chronic obstructive pulmonary disease genome-wide association loci. Am J Respir Crit Care Med. 2018;197(10):1275–84.
Article
CAS
Google Scholar
Goodman SJ, Burton CL, Butcher DT, Siu MT, Lemire M, Chater-Diehl E, et al. Obsessive-compulsive disorder and attention-deficit/hyperactivity disorder: distinct associations with DNA methylation and genetic variation. J Neurodev Disord. 2020;12(1):23.
Article
Google Scholar
Huan T, Joehanes R, Song C, Peng F, Guo Y, Mendelson M, et al. Genome-wide identification of DNA methylation QTLs in whole blood highlights pathways for cardiovascular disease. Nat Commun. 2019;10(1):4267.
Article
Google Scholar
Watanabe K, Stringer S, Frei O, Umicevic Mirkov M, de Leeuw C, Polderman TJC, et al. A global overview of pleiotropy and genetic architecture in complex traits. Nat Genet. 2019;51(9):1339–48.
Article
CAS
Google Scholar
Fortunato A, Boddy A, Mallo D, Aktipis A, Maley CC, Pepper JW. Natural selection in cancer biology: from molecular snowflakes to trait hallmarks. Cold Spring Harb Perspect Med. 2017;7(2):a.029652.
Finucane HK, Bulik-Sullivan B, Gusev A, Trynka G, Reshef Y, Loh PR, et al. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nat Genet. 2015;47(11):1228–35.
Article
CAS
Google Scholar
Sudlow C, Gallacher J, Allen N, Beral V, Burton P, Danesh J, et al. UK biobank: an open access resource for identifying the causes of a wide range of complex diseases of middle and old age. PLoS Med. 2015;12(3):e1001779.
Article
Google Scholar
Waterland RA, Kellermayer R, Laritsky E, Rayco-Solon P, Harris RA, Travisano M, et al. Season of conception in rural Gambia affects DNA methylation at putative human metastable epialleles. PLoS Genet. 2010;6(12):e1001252.
Article
CAS
Google Scholar
Silver MJ, Kessler NJ, Hennig BJ, Dominguez-Salas P, Laritsky E, Baker MS, et al. Independent genomewide screens identify the tumor suppressor VTRNA2-1 as a human epiallele responsive to periconceptional environment. Genome Biol. 2015;16:118.
Article
Google Scholar
Wells JN, Feschotte C. A field guide to eukaryotic transposable elements. Annu Rev Genet. 2020;54:539–61.
Article
CAS
Google Scholar
Van Baak TE, Coarfa C, Dugue PA, Fiorito G, Laritsky E, Baker MS, et al. Epigenetic supersimilarity of monozygotic twin pairs. Genome Biol. 2018;19(1):2.
Article
Google Scholar
Guo H, Zhu P, Yan L, Li R, Hu B, Lian Y, et al. The DNA methylation landscape of human early embryos. Nature. 2014;511(7511):606–10.
Article
CAS
Google Scholar
Yoder JA, Walsh CP, Bestor TH. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 1997;13(8):335–40.
Article
CAS
Google Scholar
Rakyan VK, Chong S, Champ ME, Cuthbert PC, Morgan HD, Luu KV, et al. Transgenerational inheritance of epigenetic states at the murine Axin(Fu) allele occurs after maternal and paternal transmission. Proc Natl Acad Sci U S A. 2003;100(5):2538–43.
Article
CAS
Google Scholar
Dugue PA, Yu C, McKay T, Wong EM, Joo JE, Tsimiklis H, et al. VTRNA2-1: genetic variation, heritable methylation and disease association. Int J Mol Sci. 2021;22(5):2535.
Elmer JL, Hay AD, Kessler NJ, Bertozzi TM, Ainscough EAC, Ferguson-Smith AC. Genomic properties of variably methylated retrotransposons in mouse. Mob DNA. 2021;12(1):6.
Article
CAS
Google Scholar
Hannon E, Mansell G, Walker E, Nabais MF, Burrage J, Kepa A, et al. Assessing the co-variability of DNA methylation across peripheral cells and tissues: implications for the interpretation of findings in epigenetic epidemiology. PLoS Genet. 2021;17(3):e1009443.
Article
CAS
Google Scholar
Trubetskoy V, Pardinas AF, Qi T, Panagiotaropoulou G, Awasthi S, Bigdeli TB, et al. Mapping genomic loci implicates genes and synaptic biology in schizophrenia. Nature. 2022;604(7906):502–8.
Article
CAS
Google Scholar
Gunasekara CJ, Waterland RA. A new era for epigenetic epidemiology. Epigenomics. 2019;11(15):1647–9.
Article
CAS
Google Scholar
Marttila S, Viiri LE, Mishra PP, Kuhnel B, Matias-Garcia PR, Lyytikainen LP, et al. Methylation status of nc886 epiallele reflects periconceptional conditions and is associated with glucose metabolism through nc886 RNAs. Clin Epigenetics. 2021;13(1):143.
Article
CAS
Google Scholar
Candler T, Kessler NJ, Gunasekara CJ, Ward KA, James P, Laritsky E, et al. DNA methylation at a nutritionally sensitive region of the PAX8 gene is associated with thyroid volume and function in Gambian children. Sci Adv. 2021;7(45):eabj1561.
Article
CAS
Google Scholar
Caramaschi D, Neumann A, Cardenas A, Tindula G, Alemany S, Zillich L, et al. Meta-analysis of epigenome-wide associations between DNA methylation at birth and childhood cognitive skills. Mol Psychiatry. 2022;27:2126-35.
Gonseth S, Shaw GM, Roy R, Segal MR, Asrani K, Rine J, et al. Epigenomic profiling of newborns with isolated orofacial clefts reveals widespread DNA methylation changes and implicates metastable epiallele regions in disease risk. Epigenetics. 2019;14(2):198–213.
Article
Google Scholar
Gunasekara CJ, Hannon E, MacKay H, Coarfa C, McQuillin A, Clair DS, et al. A machine learning case-control classifier for schizophrenia based on DNA methylation in blood. Transl Psychiatry. 2021;11(1):412.
Article
CAS
Google Scholar
Howe CG, Cox B, Fore R, Jungius J, Kvist T, Lent S, et al. Maternal gestational diabetes mellitus and newborn DNA methylation: findings from the pregnancy and childhood epigenetics consortium. Diabetes Care. 2020;43(1):98–105.
Article
CAS
Google Scholar
van Dijk SJ, Peters TJ, Buckley M, Zhou J, Jones PA, Gibson RA, et al. DNA methylation in blood from neonatal screening cards and the association with BMI and insulin sensitivity in early childhood. Int J Obes. 2018;42(1):28–35.
Article
Google Scholar
Zhu Y, Gomez JA, Laufer BI, Mordaunt CE, Mouat JS, Soto DC, et al. Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism. Genome Biol. 2022;23(1):46.
Article
CAS
Google Scholar
Zhang C, Ostrom QT, Hansen HM, Gonzalez-Maya J, Hu D, Ziv E, et al. European genetic ancestry associated with risk of childhood ependymoma. Neuro-Oncology. 2020;22(11):1637–46.
Article
CAS
Google Scholar
Wei CH, Allot A, Leaman R, Lu Z. PubTator central: automated concept annotation for biomedical full text articles. Nucleic Acids Res. 2019;47(W1):W587–93.
Article
CAS
Google Scholar
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–2.
Article
CAS
Google Scholar
Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for bisulfite-Seq applications. Bioinformatics. 2011;27(11):1571–2.
Article
CAS
Google Scholar
Shabalin AA. Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics. 2012;28(10):1353–8.
Article
CAS
Google Scholar
Schatz MC, Philippakis AA, Afgan E, Banks E, Carey VJ, Carroll RJ, et al. Inverting the model of genomics data sharing with the NHGRI genomic data science analysis, visualization, and informatics lab-space. Cell Genom. 2022;2(1):100085.
Gunasekara CJ, MacKay H, Scott CA, Li S, Laritsky E, Baker MS, Grimm SL, Jun G, Li Y, Chen R, et al. A Genomic Atlas of Systemic Interindividual Epigenetic Variation in Humans (GTEx) Datasets dbGaP. https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001746.v2.p1. 2022.