Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet. 2010; 11(3):204–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Reik W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature. 2007; 447(7143):425–32.
Article
CAS
PubMed
Google Scholar
Zeilinger S, Kühnel 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(5):1–14.
Article
CAS
Google Scholar
Robertson KD. DNA methylation and human disease. Nat Rev Genet. 2005; 6(8):597–610.
Article
CAS
PubMed
Google Scholar
Fuchikami M, Morinobu S, Segawa M, Okamoto Y, Yamawaki S, Ozaki N, Inoue T, Kusumi I, Koyama T, Tsuchiyama K, Terao T. DNA methylation profiles of the Brain-Derived Neurotrophic Factor (BDNF) gene as apotent diagnostic biomarker in major depression. PLoS ONE. 2011; 6(8):1–7.
Article
CAS
Google Scholar
Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, Delano D, Zhang L, Schroth GP, Gunderson KL, Fan JB, Shen R. High density DNA methylation array with single CpG site resolution. Genomics. 2011; 98(4):288–95.
Article
CAS
PubMed
Google Scholar
Moran S, Arribas C, Esteller M. Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences. Epigenomics. 2016; 8(3):389–99. https://doi.org/10.2217/epi.15.114.
Article
CAS
PubMed
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
PubMed
PubMed Central
Google Scholar
Liu J, Morgan M, Hutchison K, Calhoun VD. A study of the influence of sex on genome wide methylation. PLoS ONE. 2010; 5(4):1–8.
CAS
Google Scholar
Yousefi P, Huen K, Davé V, Barcellos L, Eskenazi B, Holland N. Sex differences in DNA methylation assessed by 450K BeadChip in newborns. BMC Genomics. 2015; 16(1):1–12.
Article
CAS
Google Scholar
Toker L, Feng M, Pavlidis P. Whose sample is it anyway? Widespread misannotation of samples in transcriptomics studies. F1000Research. 2016; 5:1–15.
Article
CAS
Google Scholar
Heiss JA, Just AC. Identifying mislabeled and contaminated DNA methylation microarray data: An extended quality control toolset with examples from GEO. Clin Epigenetics. 2018; 10(1):1–9.
Article
CAS
Google Scholar
McCarthy NS, Melton PE, Cadby G, Yazar S, Franchina M, Moses EK, Mackey DA, Hewitt AW. Meta-analysis of human methylation data for evidence of sex-specific autosomal patterns. BMC Genomics. 2014; 15(1):981. https://doi.org/10.1186/1471-2164-15-981.
Article
PubMed
PubMed Central
CAS
Google Scholar
Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA. Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics. 2014; 30(10):1363–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jung C-H, Park DJ, Georgeson P, Mahmood K, Milne RL, Southey MC, Pope BJ. sEst: Accurate Sex-Estimation and Abnormality Detection in Methylation Microarray Data. Int J Mol Sci. 2018; 19(10):3172.
Article
PubMed Central
CAS
Google Scholar
Hannon E, Knox O, Sugden K, Burrage J, Wong CCY, Belsky DW, Corcoran DL, Arseneault L, Moffitt TE, Caspi A, Mill J. Characterizing genetic and environmental influences on variable DNA methylation using monozygotic and dizygotic twins. PLoS Genet. 2018; 14(8):1007544.
Article
CAS
Google Scholar
Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, et al. Landscape of X chromosome inactivation across human tissues. Nature. 2017; 550(7675):244–8.
Article
PubMed
PubMed Central
Google Scholar
McCartney DL, Walker RM, Morris SW, McIntosh AM, Porteous DJ, Evans KL. Identification of polymorphic and off-target probe binding sites on the illumina infinium methylationepic beadchip. Genomics Data. 2016; 9:22–4. https://doi.org/10.1016/j.gdata.2016.05.012.
Article
PubMed
PubMed Central
Google Scholar
Abdi H, Williams LJ. Principal component analysis. Wiley Interdiscip Rev Comput Stat. 2010; 2(4):433–59.
Article
Google Scholar
Riboli E, Hunt KJ, Slimani N, Ferrari P, Norat T, Fahey M, Charrondière UR, Hémon B, Casagrande C, Vignat J, Overvad K, Tjønneland A, Clavel-Chapelon F, Thiébaut A, Wahrendorf J, Boeing H, Trichopoulos D, Trichopoulou A, Vineis P, Palli D, Bueno-de-Mesquita HB, Peeters PHM, Lund E, Engeset D, González CA, Barricarte A, Berglund G, Hallmans G, Day NE, Key TJ, Kaaks R, Saracci R. European Prospective Investigation into Cancer and Nutrition (EPIC): study populations and data collection. Public Health Nutr. 2002; 5(6b):1113–24.
Article
CAS
PubMed
Google Scholar
Zhang X, Hong D, Ma S, Ward T, Ho M, Pattni R, Duren Z, Stankov A, Shrestha SB, Hallmayer J, Wong WH, Reiss AL, Urban AE. Integrated functional genomic analyses of Klinefelter and Turner syndromes reveal global network effects of altered X chromosome dosage. Proc Natl Acad Sci U S A. 2020; 117(9):4864–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Joshi RSS, Garg P, Zaitlen N, Lappalainen T, Watson CTT, Azam N, Ho D, Li X, Antonarakis SEE, Brunner HGG, Buiting K, Cheung SWW, Coffee B, Eggermann T, Francis D, Geraedts JPP, Gimelli G, Jacobson SGG, Le Caignec C, de Leeuw N, Liehr T, Mackay DJJ, Montgomery SBB, Pagnamenta ATT, Papenhausen P, Robinson DOO, Ruivenkamp C, Schwartz C, Steiner B, Stevenson DAA, Surti U, Wassink T, Sharp AJJ. DNA methylation profiling of uniparental disomy subjects provides a map of parental epigenetic bias in the human genome. Am J Hum Genet. 2016; 99(3):555–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Walker RF, Liu JS, Peters BA, Ritz BR, Wu T, Ophoff RA, Horvath S. Epigenetic age analysis of children who seem to evade aging. Aging. 2015; 7(5):334–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Viana J, Pidsley R, Troakes C, Spiers H, Wong CCY, Al-Sarraj S, Craig I, Schalkwyk L, Mill J. Epigenomic and transcriptomic signatures of a Klinefelter syndrome (47,XXY) karyotype in the brain. Epigenetics. 2014; 9(4):587–99.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zannas AS, Jia M, Hafner K, Baumert J, Wiechmann T, Pape JC, Arloth J, Ködel M, Martinelli S, Roitman M, Röh S, Haehle A, Emeny RT, Iurato S, Carrillo-Roa T, Lahti J, Räikkönen K, Eriksson JG, Drake AJ, Waldenberger M, Wahl S, Kunze S, Lucae S, Bradley B, Gieger C, Hausch F, Smith AK, Ressler KJ, Müller-Myhsok B, Ladwig KH, Rein T, Gassen NC, Binder EB. Epigenetic upregulation of FKBP5 by aging and stress contributes to NF- κB-driven inflammation and cardiovascular risk. Proc Natl Acad Sci U S A. 2019; 166(23):11370–9.
Article
CAS
Google Scholar
Szilágyi KL, Liu C, Zhang X, Wang T, Fortman JD, Zhang W, Garcia JGN. Epigenetic contribution of the myosin light chain kinase gene to the risk for acute respiratory distress syndrome. Transl Res. 2017; 180:12–21.
Article
PubMed
CAS
Google Scholar
Uddin M, Ratanatharathorn A, Armstrong D, Kuan PF, Aiello AE, Bromet EJ, Galea S, Koenen KC, Luft B, Ressler KJ, Wildman DE, Nievergelt CM, Smith A. Epigenetic meta-analysis across three civilian cohorts identifies NRG1 and HGS as blood-based biomarkers for post-traumatic stress disorder. Epigenomics. 2018; 10(12):1585–601.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lehne B, Drong AW, Loh M, Zhang W, Scott WR, Tan ST, Afzal U, Scott J, Jarvelin MR, Elliott P, McCarthy MI, Kooner JS, Chambers JC. A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies. Genome Biol. 2015; 16(1):1–12.
Article
CAS
Google Scholar
Ventham NT, Kennedy NA, Adams AT, Kalla R, Heath S, O’Leary KR, Drummond H, Lauc G, Campbell H, McGovern DPB, Annese V, et al. Integrative epigenome-wide analysis demonstrates that DNA methylation may mediate genetic risk in inflammatory bowel disease. Nat Commun. 2016; 7(1):13507.
Article
CAS
PubMed
PubMed Central
Google Scholar
Torabi Moghadam B, Etemadikhah M, Rajkowska G, Stockmeier C, Grabherr M, Komorowski J, Feuk L, Carlström EL. Analyzing DNA methylation patterns in subjects diagnosed with schizophrenia using machine learning methods. J Psychiatr Res. 2019; 114:41–7.
Article
PubMed
Google Scholar
Wockner LF, Noble EP, Lawford BR, Young RM, Morris CP, Whitehall VLJ, Voisey J. Genome-wide DNA methylation analysis of human brain tissue from schizophrenia patients. Transl Psychiatry. 2014; 4(1):339.
Article
CAS
Google Scholar
Cederlöf M, Gotby] AO, Larsson H, Serlachius E, Boman M, Långström N, Landén M, Lichtenstein P. Klinefelter syndrome and risk of psychosis, autism and ADHD. J Psychiatr Res. 2014; 48(1):128–30.
Article
PubMed
Google Scholar
LYON MF. Gene action in the X-chromosome of the mouse (Mus musculus L.)Nature. 1961; 190(4773):372–3.
Article
CAS
PubMed
Google Scholar
Sharp AJ, Stathaki E, Migliavacca E, Brahmachary M, Montgomery SB, Dupre Y, Antonarakis SE. DNA methylation profiles of human active and inactive X chromosomes. Genome Res. 2011; 21(10):1592–600.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jaffe AE, Irizarry RA. Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol. 2014; 15(2):1–9.
Article
Google Scholar
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(1):86.
Article
PubMed
PubMed Central
Google Scholar
Burton GJ, Fowden AL. The placenta: a multifaceted, transient organ. Philos Trans R Soc B Biol Sci. 2015; 370(1663):20140066.
Article
Google Scholar
Guo H, Zhu P, Yan L, Li R, Hu B, Lian Y, Yan J, Ren X, Lin S, Li J, Jin X, Shi X, Liu P, Wang X, Wang W, Wei Y, Li X, Guo F, Wu X, Fan X, Yong J, Wen L, Xie SX, Tang F, Qiao J. The DNA methylation landscape of human early embryos. Nature. 2014; 511(7511):606–10.
Article
CAS
PubMed
Google Scholar
Pidsley R, Y Wong CC, Volta M, Lunnon K, Mill J, Schalkwyk LC. A data-driven approach to preprocessing Illumina 450K methylation array data. BMC Genomics. 2013; 14(1):293.
Article
CAS
PubMed
PubMed Central
Google Scholar
Virtanen P, Gommers R, Oliphant TE, Haberland M, Reddy T, Cournapeau D, Burovski E, Peterson P, Weckesser W, Bright J, van der Walt SJ, Brett M, Wilson J, Millman KJ, Mayorov N, Nelson ARJ, Jones E, Kern R, Larson E, Carey CJ, Polat İ, Feng Y, Moore EW, VanderPlas J, Laxalde D, Perktold J, Cimrman R, Henriksen I, Quintero EA, Harris CR, Archibald AM, Ribeiro AH, Pedregosa F, van Mulbregt P, SciPy 1.0 Contributors. SciPy 1.0: Fundamental Algorithms for Scientific Computing in Python. Nat Methods. 2020; 17:261–72. https://doi.org/10.1038/s41592-019-0686-2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, Blondel M, Prettenhofer P, Weiss R, Dubourg V, Vanderplas J, Passos A, Cournapeau D, Brucher M, Perrot M, Duchesnay E. Scikit-learn: Machine learning in Python. J Mach Learn Res. 2011; 12:2825–30.
Google Scholar
Hannon E, Mansell G, Burrage J, Kepa A, Best-Lane J, Rose A, Heck S, Moffitt T, Caspi A, Arseneault L, Mill J. Assessing the co-variability of DNA methylation across peripheral cells and tissues: implications for the interpretation of findings in epigenetic epidemiology. bioRxiv. 2020.05.21.107730. https://doi.org/10.1101/2020.05.21.107730.
Mcewen LM, Donnell KJO, Mcgill MG, Edgar RD, Jones MJ, Macisaac JL, Lin DTS, Ramadori KE, Morin AM, Gladish N, Garg E, Unternaehrer E, Pokhvisneva I, Karnani N, Lee M, Klengel T, Adler N, Barr RG, Letourneau N, Giesbrecht GF, Reynolds JN, Czamara D, Armstrong JM, Essex MJ, de Weerth C, Beijers R, Tollenaar MS, Bradley B, Jovanovic T, Ressler KJ, Steiner M, Entringer S, Wadhwa PD, Buss C, Bush NR, Binder EB, Boyce WT, Meaney MJ, Horvath S, Kobor MS. The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells. Proc Natl Acad Sci U S A. 2019:1–7.
Pai S, Li P, Killinger B, Marshall L, Jia P, Liao J, Petronis A, Szabó PE, Labrie V. Differential methylation of enhancer at IGF2 is associated with abnormal dopamine synthesis in major psychosis. Nat Commun. 2019; 10(1):2046.
Article
PubMed
PubMed Central
CAS
Google Scholar
Horvath S, Gurven M, Levine ME, Trumble BC, Kaplan H, Allayee H, Ritz BR, Chen B, Lu AT, Rickabaugh TM, Jamieson BD, Sun D, Li S, Chen W, Quintana-Murci L, Fagny M, Kobor MS, Tsao PS, Reiner AP, Edlefsen KL, Absher D, Assimes TL. An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease. Genome Biol. 2016; 17(1):22.
Article
CAS
Google Scholar
Wang L, Marek GW, Hlady RA, Wagner RT, Zhao X, Clark VC, Fan AX, Liu C, Brantly M, Robertson KD. Alpha-1 antitrypsin deficiency liver disease, mutational homogeneity modulated by epigenetic heterogeneity with links to obesity. Hepatology. 2019; 70(1):51–66.
CAS
PubMed
Google Scholar
Wilson SL, Leavey K, Cox BJ, Robinson WP. Mining DNA methylation alterations towards a classification of placental pathologies. Hum Mol Genet. 2017; 27(1):135–46.
Article
PubMed Central
CAS
Google Scholar
Jenkins TG, Aston KI, Trost C, Farley J, Hotaling JM, Carrell DT. Intra-sample heterogeneity of sperm DNA methylation. Mol Hum Reprod. 2014; 21(4):313–9.
Article
PubMed
CAS
Google Scholar
The UK Household Longitudinal Study. https://www.understandingsociety.ac.uk/about/about-the-study. Accessed 30 Dec 2020.