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Epigenome Data Production

The International Human Epigenome Consortium (IHEC) has been producing the 1000 reference epigenome map on 250 human cell types to decipher key cellular states relevant to human health and diseases. The KES(Korea Epigenome Study) was launched in accordance with the IHEC in 2012 to produce 50 epigenomic datasets on complex disease-related target cells from the Korean population. The objective of the KES was to provide a comprehensive epigenomic map of complex disease-related target tissues from Koreans to unravel the causality of chronic diseases through epigenome research[Figure3].

Organization of the Korea Epigenome Study

Figure3.  Organization of the Korea Epigenome Study

To achieve this goal, single cells were isolated from the pancreas, fat, and kidney. Each cell type was derived from normal tissues or those from clinical cases with diabetes, obesity, or chronic kidney disease. In addition, primary tissue culture samples started to be collected and banked with the aim of facilitating supply on the production of an epigenome map.
In 2015, KES started to produce 19 new reference epigenome datasets of pancreatic, fat, and kidney cells. Cell types, such as the islets and beta cells from the pancreas, adipocytes and preadipocytes from fat tissue, and podocytes and mesangial cells from the kidneys, were used as primary targets. The production of the primary cell epigenome map began on cell types of agerelated fibroblast and various induced pluripotent stem (iPS) cells through the project “Primary cell epigenome data production from Koreans.” Data from whole-genome bisulfite sequencing(WGBS), Infinium 450k DNA methylation bead array, mRNA sequencing, and miRNA sequencing was generated to fulfill IHEC standard. ChIP-seq data was also generated through the project “Production of diabetes-related histone binding genome information.”  The standardization, quality control, and construction of a comprehensive epigenomic map from the dataset will be completed next year. With the collaboration of the IHEC, the KNIH helped to develop assay standards, metadata, data ecosystems, bioethics and communication, and in developing standard protocols for the IHEC epigenome data production and collaboration [Figure4].

Timeline of the Korea Epigenome Study
Figure4. Timeline of the Korea Epigenome Study