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Perspective papers on the future of epigenome research

A series of recent papers discuss current standards and future perspectives for epigenome research, particularly with a focus on cancer and disease-centric epigenome association studies:

  • Bock C (2014). Synergy and competition between cancer genome sequencing and epigenome mapping projects. Genome Medicine 6, 41. [Comment article outlining the interplay between cancer genome & epigenome projects]

    Abstract: Large-scale projects in the fields of cancer genomics and epigenomics have different aims, cultures and outcomes. The author argues that by working together a complete picture of cancer biology could be painted, and he advocates the creation of an International Cancer Epigenome Consortium.

    http://genomemedicine.com/content/6/5/41 (no digital access? A reprint is available on request)


  • Almouzni G, Altucci L, Amati B, Ashley N, Baulcombe D, Beaujean N, Bock C, Bongcam-Rudloff E, Bousquet J, Braun S, de Paillerets BB, Bussemakers M, Clarke L, Conesa A, Estivill X, Fazeli A, Grgurevi NA, Gut I, Heijmans BT, Hermouet S, Houwing Duistermaat J, Iacobucci I, Ila J, Kandimalla R, Krauss-Etschmann S, Lasko P, Lehmann S, Lindroth A, Majdi G, Marcotte E, Martinelli G, Martinet N, Meyer E, Miceli C, Mills K, Moreno-Villanueva M, Morvan G, Nickel D, Niesler B, Nowacki M, Nowak J, Ossowski S, Pelizzola M, Pochet R, Poto Nik U, Radwanska M, Raes J, Rattray M, Robinson MD, Roelen B, Sauer S, Schinzer D, Slagboom E, Spector T, Stunnenberg HG, Tiligada E, Torres-Padilla ME, Tsonaka R, Van Soom A, Vidakovi M, Widschwendter M (2014). Relationship between genome and epigenome - challenges and requirements for future research. BMC Genomics 15, 487. [EU workshop report on strategy in genome and epigenome research]

    Abstract: Understanding the links between genetic, epigenetic and non-genetic factors throughout the lifespan and across generations and their role in disease susceptibility and disease progression offer entirely new avenues and solutions to major problems in our society. To overcome the numerous challenges, we have come up with nine major conclusions to set the vision for future policies and research agendas at the European level.

    http://www.biomedcentral.com/1471-2164/15/487 (open access article)


  • Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, Houseman EA, Izzi B, Kelsey KT, Meissner A, Milosavljevic A, Siegmund KD, Bock C, Irizarry RA (2013). Recommendations for the design and analysis of epigenome-wide association studies. Nature Methods 10, 949-955. 

    Abstract: Epigenome-wide association studies (EWAS) hold promise for the detection of new regulatory mechanisms that may be susceptible to modification by environmental and lifestyle factors affecting susceptibility to disease. Epigenome-wide screening methods cover an increasing number of CpG sites, but the complexity of the data poses a challenge to separating robust signals from noise. Appropriate study design, a detailed a priori analysis plan and validation of results are essential to minimize the danger of false positive results and contribute to a unified approach. Epigenome-wide mapping studies in homogenous cell populations will inform our understanding of normal variation in the methylome that is not associated with disease or aging. Here we review concepts for conducting a stringent and powerful EWAS, including the choice of analyzed tissue, sources of variability and systematic biases, outline analytical solutions to EWAS-specific problems and highlight caveats in interpretation of data generated from samples with cellular heterogeneity.

    http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2632.html (no digital access? A reprint is available on request)

 

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