Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study

BACKGROUND: The datafiles deposited here are products of the research project "Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study" Authors: Ayşe Demirkan1,2, Jenny van Dongen3,4, Casey T. Finnicum5, Harm-Jan Westra1, Soesma Jankipersadsing1, Gonneke Willemsen3,4, Richard G. Ijzerman6, Dorret I. Boomsma3,4, Erik A. Ehli5, Marc Jan Bonder1, Jingyuan Fu,1,7 Lude Franke1, Cisca Wijmenga1, Eco J.C. de Geus3,4, Alexander Kurilshikov1, Alexandra Zhernakova1 1 Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands 2 Section of Statistical Multi-omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine & People-Centered AI institute University of Surrey, Guildford, United Kingdom 3 Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands 4 Amsterdam Public Health Research Institute, Amsterdam, the Netherlands 5 Avera Institute of Human Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD, USA 6 Department of Endocrinology, Amsterdam University Medical Center, location VUMC, Amsterdam, the Netherlands 7 Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands Corresponding Authors: Alexandra Zhernakova; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands Ayse Demirkan; Section of Statistical Multi-omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine & People-Centered AI institute University of Surrey, Guildford, United Kingdom. FILES: 1-merged_lld16s.Rata: Epigenome-wide association of 16s microbial abundances in LifeLines-Deep (LLD, n = 616, 450k methylation array) 2-lld_mgs.Rdata: Epigenome-wide association ofshotgun metagenomic sequencing derived taxa relative abundances (n = 683, 450k methylation array)) 3-lld_mgs_pathways. Rdata: Epigenome-wide association ofshotgun metagenomic sequencing derived bacterial pathway relative abundances (n = 683, 450k methylation array) FUNDING: The Lifelines initiative has been made possible by subsidy from the Dutch Ministry of Health, Welfare and Sport, the Dutch Ministry of Economic Affairs, the University Medical Center Groningen (UMCG), Groningen University and the Provinces in the North of the Netherlands (Drenthe, Friesland, Groningen). The Netherlands Twin Register acknowledges funding from the Netherlands Organization for Scientific Research (NWO): (NWO 911–09–032; NWO 480-04-004; 480-15-001/674, NWO 916-130-82), Biobanking and Biomolecular Research Infrastructure (184.033.111), and the BBRMI-NL-financed BIOS Consortium (NWO 184.021.007), NWO Large Scale infrastructures X-Omics (184.034.019), Genotype/phenotype database for behaviour genetic and genetic epidemiological studies (ZonMw Middelgroot 911-09-032); Netherlands Twin Registry Repository: researching the interplay between genome and environment (NWO-Groot 480-15-001/674); the Avera Institute, Sioux Falls (USA), the European Research Council (Genetics of Mental Illness 230374), the European Research Council (Genetics of Mental Illness 230374), and INRA-Pfizer. Pfizer provided support for data collection, but did not have any additional role in the study design, data analysis, decision to publish, or preparation of the manuscript.背景：本处存档的数据文件源自研究项目「通过发现与重复全表观基因组关联研究（epigenome-wide association study），将肠道微生物组与宿主DNA甲基化建立关联」 作者：Ayşe Demirkan1,2, Jenny van Dongen3,4, Casey T. Finnicum5, Harm-Jan Westra1, Soesma Jankipersadsing1, Gonneke Willemsen3,4, Richard G. Ijzerman6, Dorret I. Boomsma3,4, Erik A. Ehli5, Marc Jan Bonder1, Jingyuan Fu1,7, Lude Franke1, Cisca Wijmenga1, Eco J.C. de Geus3,4, Alexander Kurilshikov1, Alexandra Zhernakova1 1 格罗宁根大学格罗宁根大学医学中心遗传学系，荷兰格罗宁根 2 萨里大学生物科学与医学院临床与实验医学系统计多组学科室暨以人为中心的人工智能研究所，英国吉尔福德 3 阿姆斯特丹自由大学生物心理学系，荷兰阿姆斯特丹 4 阿姆斯特丹公共卫生研究所，荷兰阿姆斯特丹 5 阿维拉人类遗传学研究所，阿维拉麦肯纳医院与大学健康中心，美国南达科他州苏福尔斯 6 阿姆斯特丹大学医学中心VUMC院区内分泌学系，荷兰阿姆斯特丹 7 格罗宁根大学格罗宁根大学医学中心儿科学系，荷兰格罗宁根 通讯作者：Alexandra Zhernakova；单位：格罗宁根大学格罗宁根大学医学中心遗传学系，荷兰格罗宁根 Ayse Demirkan；单位：萨里大学生物科学与医学院临床与实验医学系统计多组学科室暨以人为中心的人工智能研究所，英国吉尔福德 文件： 1. merged_lld16s.Rata：生命深度队列（LifeLines-Deep，LLD，n=616，采用450K甲基化芯片）中16S微生物丰度的全表观基因组关联分析 2. lld_mgs.Rdata：基于宏基因组鸟枪法测序得到的类群相对丰度的全表观基因组关联分析（n=683，采用450K甲基化芯片） 3. lld_mgs_pathways.Rdata：基于宏基因组鸟枪法测序得到的细菌代谢通路相对丰度的全表观基因组关联分析（n=683，采用450K甲基化芯片） 资助说明：生命队列（Lifelines）项目的开展得益于荷兰卫生、福利与体育部、荷兰经济事务部、格罗宁根大学医学中心（UMCG）、格罗宁根大学以及荷兰北部省份（德伦特省、弗里斯兰省、格罗宁根省）的资助。荷兰双生子登记系统的研究得到了荷兰科学研究组织（NWO）的资助，资助编号包括：NWO 911–09–032、NWO 480-04-004、480-15-001/674、NWO 916-130-82；生物样本库与生物分子研究基础设施（编号184.033.111）；由BBRMI-NL资助的BIOS联盟（NWO 184.021.007）；NWO大型基础设施项目X-Omics（编号184.034.019）；行为遗传学与遗传流行病学研究用基因型/表型数据库（ZonMw 中等规模项目 911-09-032）；荷兰双生子登记系统库：研究基因组与环境的相互作用（NWO大型项目 480-15-001/674）；美国苏福尔斯的阿维拉研究所；欧洲研究委员会（精神疾病遗传学项目，编号230374）；以及INRA-Pfizer。辉瑞公司为数据收集提供了支持，但未参与研究设计、数据分析、发表决策或稿件撰写工作。