ABOUT

Purpose of iMethyl database

  • The Human Genome Project (HGP) and 1000 Genome Project (1KGP) uncovered the genomic information and variations of individuals. Presently, much clinical and biological research is based on evidence previously generated by HGP and 1KGP. In the past two decades, researchers elucidated the relationships between diseases and genetic codes using genetic linkage analysis and genome-wide association studies (GWAS). However, in this research, most results were only obtained from the four classic bases (A, C, G, and T) of DNA. In the early 1980s, several groups reported the methylation of CpG dinucleotides and lack of methylation at promoter regions. In the late 1990s, methyl-cytosine (mC) was recognized as the fifth base. Recently, several major reports highlighted the relationship between common diseases and CpG methylation (epigenome); however, limited reference epigenome data have been published. In this database, we have included the average, standard deviations, and CpG methylation distributions of monocytes, CD4+ T cells, and neutrophils from over 100 individuals. This dataset is the first population epigenome dataset in the world. We are glad to have the opportunity to accelerate your epigenome research.    

Data Usage

  • We require that any use of data obtained from our website be sited in your publifications (see below).
  • Iwate Tohoku Medical Megabank Organization, iMethyl Database; over 100 Japanese whole genome DNA methylation database from monocytes, CD4+ T cells, and neutrophils, (access date), http://imethyl.iwate-megabank.org/
  • T. Hachiya et al. "Genome-wide identification of inter-individually variable DNA methylation sites improves the efficacy of epigenetic association studies" NPJ Genom Med. in press, 2017

Protocol for the isolation of Monocytes and CD4+ T cells from PBMCs

  • PBMCs were stained with CD14-FITC, CD16-PE, CD3-PE/Cy7, and CD4-APC antibodies (5 µL / 500 µL cell suspension; Sony Biotechnology, Inc., Tokyo, Japan) and incubated for 20 min at 4°C. After washing with a 5 × volume of PBS, CD14++/CD16- monocytes and CD3+/CD4+ T cells were immediately sorted using a CellSorter SH800 (Sony) from the monocyte- or lymphocyte-containing gate determined by light-scatter density-plot.

Protocol for the isolation of Neutrophils from Peripheral blood

  • Polymorph nuclear cells were stained with CD16-PE antibody (5 µL / 500 µL cell suspension; Sony Biotechnology, Inc., Tokyo, Japan) and incubated for 20 min at 4°C. After washing with a 5 × volume of PBS, CD16+ neutrophils were immediately sorted using a CellSorter SH800 (Sony).

Public Data Release

  • March 31, 2016. Website was launched. The first data release contained data of SNVs, CpG methylation levels (beta values), and gene expression values (FPKMs) of monocytes and CD4+ T cells from 102 individuals.
  • March 31, 2017. New tracks for neutrophils were added. In addtion, DNAm variability tracks by reference interval, which is defined as the difference between the 95th and 5th percentiles of the DNAm level found among individuals, were added.

Iwate Tohoku Medical Megabank Organization

  • Iwate Tohoku Medical Megabank Organization (IMM) uses “health” as a tie to bind medical care and areas stricken by disasters. Using health surveys and the creation of a local “biobank”, we are working to enhance and restore medical services, rebuild the community, and create healthy municipalities.
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Acknowledgment

  • This work was supported by the Tohoku Medical Megabank Project (Special Account for Reconstruction from the Great East Japan Earthquake) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) and Japan Agency for Medical Research and Development (AMED). We thank the members of the Iwate Tohoku Medical Megabank Organization of Iwate Medical University (IMM) and Tohoku Medical Megabank Organization of Tohoku University (ToMMo) for their encouragement and support, as well as the voluntary contributions of all participants. SNV data was provided from Tohoku Medical Megabank Organization of Tohoku University (ToMMo).

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