A summary of research on DNA methylation

A summary of research on DNA methylationSheng Shin skill Tree has been concerned 2018.01.23 11:43 words 993 Read 183 Comments 0 likes 1

DNA methylation (DNA methylation) is one of the first important epigenetic modifications to be studied, and high-throughput technologies based on chips and next-generation sequencing provide a technical platform for the extensive detection of DNA methylation. Including, Wgbs,rrbs,microarray (27k/450k/850k), Medip-seq,mre-seq

Methylation Chip

The Infinium humanmethylation27/450 beadchip Chip (hereinafter referred to as the 27k/450k methylation Chip) offers a comprehensive, professionally selected CPG site coverage, high-throughput sample parallel and affordable methylation assay service, Make it an ideal solution for epigenetic genome-related research. For example, the Cancer Genome Atlas (TCGA) uses the human methylation 27/450 beadchip chip to determine DNA methylation spectra in more than 12 000 samples covering 34 types of cancer. Compared with the methylation detection method based on sequencing technology, the low cost and high return characteristics of methylation 27/450 beadchip chip make it widely used and popularized, which provides a strong guarantee for the research of group methylation mode and state.

Five big public data

With the continuous development of high-throughput biotechnology (chip, sequencing technology), high-throughput DNA methylation data are emerging, and some large international collaborative big data programs have produced a PB (Petabyte) quantitative methylation spectrum. The international Human Epigenetic Genome Alliance (International Human Epigenome Consortium, a group of research institutions from a number of countries and regions, For short ihec) more than 1000 epigenetics data were produced to study the cell status associated with human health and complex diseases, including cancer

• The Roadmap epigenomics Mapping Consortium, or roadmap, funded by the U.S. NIH, produced 367 DNA methylation profiles of human major tissues and cell types
• The European "Blood Epigenetic Genome Project" (BLUEPRINT of Haematopoietic Epigenomes, abbreviated BLUEPRINT) produced a DNA methylation map of 82 different blood cells associated with human complex diseases.
• The "Encyclopedia of DNA Elements" program (The Encyclopedia of DNA Elements, abbreviated as encode) is another major international partnership after the Human Genome Project, 32 research institutes from around the world measured DNA methylation levels in 206 different human cell lines and tissues.
• The International Cancer Genome Consortium (the International Cancer Genome Consortium, abbreviated as ICGC, aims to study the occurrence and development of cancer from a multidimensional data level, such as genomics, epigenetic and transcription groups, ICGC produced DNA methylation data for more than 9,000 samples involving 27 common cancers,
• The United States Cancer Genome collection (the Cancer Genome Atlas, abbreviated TCGA) aims to study the occurrence and development of cancer from a multidimensional data level, such as genomics, epigenetics, and Transcriptome, TCGA produces DNA methylation data for more than 10,000 samples of 34 types of cancer, It also retains the detailed clinical data of cancer patients and provides a large amount of data resources for survival analysis.

Reference documents:

Laird, P.W, principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet, 2010. One (3): P. 191-203.

Cancer Genome Atlas, N., et al, the Cancer Genome Atlas Pan-cancer Analysis project. Nat Genet, 2013. (+): P. 1113-20.

Cancer genome Atlas, N., et al, comprehensive Molecular characterization of papillary renal-cell carcinoma. N Engl J Med, 2016. 374 (2): P. 135-45.

Satterlee, J.S, D. Schubeler, and H.H. Ng, tackling the epigenome:challenges and opportunities for collaboration. Nat Biotechnol, 2010. : P. 1039-44.

Roadmap Epigenomics, C., et al, integrative Analysis of 111 reference human epigenomes. Nature, 2015. 518 (7539): P. 317-30.

Adams, D., et al, BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol, 2012. (3): P. 224-6.

Consortium, E.P, an integrated encyclopedia of DNA elements in the human genome. Nature, 2012. 489 (7414): P. 57-74.

International cancer genome, C., et al, International network of Cancer genome projects. Nature, 2010. 464 (7291): P. 993-8.

A summary of research on DNA methylation