{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"contact_person":["Elin Grundberg"],"full_dataset_link":["https://ega-archive.org/dacs/EGAC00001000402"],"host":["EGA"],"description":["EGA DAC EGAC00001000402"],"repository":["EGA"],"email":["elin.grundberg@mcgill.ca"],"pubmed_abstract":["<h4>Background</h4>CpG methylation variation is involved in human trait formation and disease susceptibility. Analyses within populations have been biased towards CpG-dense regions through the application of targeted arrays. We generate whole-genome bisulfite sequencing data for approximately 30 adipose and blood samples from monozygotic and dizygotic twins for the characterization of non-genetic and genetic effects at single-site resolution.<h4>Results</h4>Purely invariable CpGs display a bimodal distribution with enrichment of unmethylated CpGs and depletion of fully methylated CpGs in promoter and enhancer regions. Population-variable CpGs account for approximately 15-20 % of total CpGs per tissue, are enriched in enhancer-associated regions and depleted in promoters, and single nucleotide polymorphisms at CpGs are a frequent confounder of extreme methylation variation. Differential methylation is primarily non-genetic in origin, with non-shared environment accounting for most of the variance. These non-genetic effects are mainly tissue-specific. Tobacco smoking is associated with differential methylation in blood with no evidence of this exposure impacting cell counts. Opposite to non-genetic effects, genetic effects of CpG methylation are shared across tissues and thus limit inter-tissue epigenetic drift. CpH methylation is rare, and shows similar characteristics of variation patterns as CpGs.<h4>Conclusions</h4>Our study highlights the utility of low pass whole-genome bisulfite sequencing in identifying methylome variation beyond promoter regions, and suggests that targeting the population dynamic methylome of tissues requires assessment of understudied intergenic CpGs distal to gene promoters to reveal the full extent of inter-individual variation."],"pubmed_title":["Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation."],"pubmed_authors":["Busche Stephan S, Shao Xiaojian X, Caron Maxime M, Kwan Tony T, Allum Fiona F, Cheung Warren A WA, Ge Bing B, Westfall Susan S, Simon Marie-Michelle MM, Barrett Amy A, Bell Jordana T JT, McCarthy Mark I MI, Deloukas Panos P, Blanchette Mathieu M, Bourque Guillaume G, Spector Timothy D TD, Lathrop Mark M, Pastinen Tomi T, Grundberg Elin E"],"pubmed_title_synonyms":["School-Age Populations, H2S(D2S), Populations, human being, Man (Taxonomy), Genomes, hydrosulfite, Modern, Tissue, bisulfite, whole genome, Population, School Age Populations, Impact, Human, Environmental Impact, Environmental, School-Age, Homo sapiens, School Age, Modern Man, Environments, Impacts, School-Age Population, School Age Population, Environmental Impacts, human., Man"],"name_synonyms":["Kaliumchlorid, [KCl], whole genome bisulfite sequencing, Klor-con, muriate of potash, WGBS, Klotrix, Kaon-Cl 10, KCl, Monopotassium chloride, sylvite, Shotgun bisulfite sequencing., whole-genome shotgun bisulfite sequencing, WGSBS"],"pubmed_abstract_synonyms":["extent, H2S(D2S), d230, BODYFAT, human being, Materials, Diatheses, supply, Gene, disease susceptibilities, dTAFII250, Gm695, fat, EfW1, Human, dmTAF[[II]]230, School-Age, Susceptibility, Homo sapiens, dmTAF1, Taf230, Twin, Impacts, Tobacco, Low, Cph1, Environmental Impacts, fatty tissue, Man, fat tissue, multicellular organismal biosynthetic process, TAF250, School-Age Populations, study, single-organism biosynthetic process, Taf200, me75, dTAF[[II]]250, Man (Taxonomy), Genetic, TFIID TAF250, Genomes, adipose system, cel, distribution, cell, Accountings, Tissue, bisulfite, Taf1p, Population, D17Mit170, T1, Epigenomic, genetic, Environmental Impact, dTAF250, high frequency, diathesis, Carboxypeptidase H, bodyfat, site, School Age Population, associated, Nucleotide, TAF, constitutitional genetic, CPE, CPH, Methylations, Disease, dTAF[[II]]230, TAF[[II]]250, Diathesis, cou, whole blood, hydrosulfite, R74677, Modern, familial, TAF200, Prohormone-processing carboxypeptidase, l(3)84Ab, BG:DS00004.13, TAFII-250, TAF250/230, Tl3, Tl2, Cistrons, results, Cell, Impact, dTAF230, Environmental, Body Fat, TAFII250, Lr, adp, School Age, p230, TAF[[II]]250/230, TFIID, Genetic Materials, simple tissue, rare (European definition), background, methylation, supply and distribution, Enkephalin convertase, Cph-1, region, INSDC_feature:regulatory, Genetic Material, nucleotides, Smoking, Taf[[II]]250, susceptibility, Populations, tobacco use disorder, Disease Susceptibilities, TAF[[II]]230, frequent, Epigenetic, completeness., 3.4.17.10, TAF[II]250, INSDC_feature:gene, whole genome, CG17603, TAF[[II]], School Age Populations, human, introduction, Susceptibilities, Tobacco Smoking, diatheses, disease, DmelCG17603, fatty depot, Taf250, adipose, Material, SR3-5, Modern Man, Environments, Bra, Cistron, inherited genetic, School-Age Population, variable, Epigenetics, susceptibilities, hereditary, TAF230, TAF1"],"additional_accession":[]},"is_claimable":false,"name":"McGill-KCL WGBS","description":"Data Access Committee EGAC00001000402","dates":{"output":"2025-1-9"},"accession":"EGAC00001000402","cross_references":{"TAXONOMY":["9606"],"pubmed":["26699896"],"EGA":["EGAS00001001569","EGAD00001001688","EGAD00001001689"]}}