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Epigenomics of Disease

Genome Biology Collection

Epigenomics of diseaseThe epigenome has been shown to change significantly during progression of diseases and during aging. These epigenetic changes are often shown to be associated with changes in gene expression. Through analysis of these changes, useful biomarkers can be discovered and we can better understand mechanisms of disease progression or cancer heterogeneity.

In this collection, Genome Biology highlights recently published papers related to disease-associated DNA methylation changes.

  1. Method

    cepip: context-dependent epigenomic weighting for prioritization of regulatory variants and disease-associated genes

    It remains challenging to predict regulatory variants in particular tissues or cell types due to highly context-specific gene regulation. By connecting large-scale epigenomic profiles to expression quantitativ...

    Mulin Jun Li, Miaoxin Li, Zipeng Liu, Bin Yan, Zhicheng Pan, Dandan Huang, Qian Liang, Dingge Ying, Feng Xu, Hongcheng Yao, Panwen Wang, Jean-Pierre A. Kocher, Zhengyuan Xia, Pak Chung Sham, Jun S. Liu and Junwen Wang

    Genome Biology 2017 18:52

    Published on: 16 March 2017

  2. METHOD

    epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data

    The study of epigenetic heterogeneity at the level of individual cells and in whole populations is the key to understanding cellular differentiation, organismal development, and the evolution of cancer. We dev...

    Martin Vincent, Kamilla Mundbjerg, Jakob Skou Pedersen, Gangning Liang, Peter A. Jones, Torben Falck Ørntoft, Karina Dalsgaard Sørensen and Carsten Wiuf

    Genome Biology 2017 18:38

    Published on: 21 February 2017

  3. Research

    Single-cell epigenomic variability reveals functional cancer heterogeneity

    Cell-to-cell heterogeneity is a major driver of cancer evolution, progression, and emergence of drug resistance. Epigenomic variation at the single-cell level can rapidly create cancer heterogeneity but is dif...

    Ulrike M. Litzenburger, Jason D. Buenrostro, Beijing Wu, Ying Shen, Nathan C. Sheffield, Arwa Kathiria, William J. Greenleaf and Howard Y. Chang

    Genome Biology 2017 18:15

    Published on: 24 January 2017

  4. Research

    Identifying aggressive prostate cancer foci using a DNA methylation classifier

    Slow-growing prostate cancer (PC) can be aggressive in a subset of cases. Therefore, prognostic tools to guide clinical decision-making and avoid overtreatment of indolent PC and undertreatment of aggressive d...

    Kamilla Mundbjerg, Sameer Chopra, Mehrdad Alemozaffar, Christopher Duymich, Ranjani Lakshminarasimhan, Peter W. Nichols, Manju Aron, Kimberly D. Siegmund, Osamu Ukimura, Monish Aron, ‬Mariana Stern, Parkash Gill, John D. Carpten, Torben F. Ørntoft, Karina D. Sørensen, Daniel J. Weisenberger…

    Genome Biology 2017 18:3

    Published on: 12 January 2017

  5. Method

    DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases

    Chronic low-grade inflammation reflects a subclinical immune response implicated in the pathogenesis of complex diseases. Identifying genetic loci where DNA methylation is associated with chronic low-grade inf...

    Symen Ligthart, Carola Marzi, Stella Aslibekyan, Michael M. Mendelson, Karen N. Conneely, Toshiko Tanaka, Elena Colicino, Lindsay L. Waite, Roby Joehanes, Weihua Guan, Jennifer A. Brody, Cathy Elks, Riccardo Marioni, Min A. Jhun, Golareh Agha, Jan Bressler…

    Genome Biology 2016 17:255

    Published on: 12 December 2016

  6. Research Highlight

    A new timepiece: an epigenetic mitotic clock

    A new mitotic clock and mathematical approach that incorporates DNA methylation biology common among human cell types provides a new tool for cancer epigenetics research.

    Brock C. Christensen and Karl T. Kelsey

    Genome Biology 2016 17:216

    Published on: 19 October 2016

  7. Research

    Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling

    In recent years the Illumina HumanMethylation450 (HM450) BeadChip has provided a user-friendly platform to profile DNA methylation in human samples. However, HM450 lacked coverage of distal regulatory elements...

    Ruth Pidsley, Elena Zotenko, Timothy J. Peters, Mitchell G. Lawrence, Gail P. Risbridger, Peter Molloy, Susan Van Djik, Beverly Muhlhausler, Clare Stirzaker and Susan J. Clark

    Genome Biology 2016 17:208

    Published on: 7 October 2016

  8. Research

    Correlation of an epigenetic mitotic clock with cancer risk

    Variation in cancer risk among somatic tissues has been attributed to variations in the underlying rate of stem cell division. For a given tissue type, variable cancer risk between individuals is thought to be...

    Zhen Yang, Andrew Wong, Diana Kuh, Dirk S. Paul, Vardhman K. Rakyan, R. David Leslie, Shijie C. Zheng, Martin Widschwendter, Stephan Beck and Andrew E. Teschendorff

    Genome Biology 2016 17:205

    Published on: 3 October 2016

  9. Research

    Novel regional age-associated DNA methylation changes within human common disease-associated loci

    Advancing age progressively impacts on risk and severity of chronic disease. It also modifies the epigenome, with changes in DNA methylation, due to both random drift and variation within specific functional l...

    Christopher G. Bell, Yudong Xia, Wei Yuan, Fei Gao, Kirsten Ward, Leonie Roos, Massimo Mangino, Pirro G. Hysi, Jordana Bell, Jun Wang and Timothy D. Spector

    Genome Biology 2016 17:193

    Published on: 23 September 2016

  10. Research

    Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms

    Epigenetic change is a hallmark of ageing but its link to ageing mechanisms in humans remains poorly understood. While DNA methylation at many CpG sites closely tracks chronological age, DNA methylation change...

    Roderick C. Slieker, Maarten van Iterson, René Luijk, Marian Beekman, Daria V. Zhernakova, Matthijs H. Moed, Hailiang Mei, Michiel van Galen, Patrick Deelen, Marc Jan Bonder, Alexandra Zhernakova, André G. Uitterlinden, Ettje F. Tigchelaar, Coen D. A. Stehouwer, Casper G. Schalkwijk, Carla J. H. van der Kallen…

    Genome Biology 2016 17:191

    Published on: 22 September 2016

  11. Research

    An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation

    Schizophrenia is a highly heritable, neuropsychiatric disorder characterized by episodic psychosis and altered cognitive function. Despite success in identifying genetic variants associated with schizophrenia,...

    Eilis Hannon, Emma Dempster, Joana Viana, Joe Burrage, Adam R. Smith, Ruby Macdonald, David St Clair, Colette Mustard, Gerome Breen, Sebastian Therman, Jaakko Kaprio, Timothea Toulopoulou, Hilleke E. Hulshoff Pol, Marc M. Bohlken, Rene S. Kahn, Igor Nenadic…

    Genome Biology 2016 17:176

    Published on: 30 August 2016

  12. Research

    An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease

    Epigenetic biomarkers of aging (the “epigenetic clock”) have the potential to address puzzling findings surrounding mortality rates and incidence of cardio-metabolic disease such as: (1) women consistently exh...

    Steve Horvath, Michael Gurven, Morgan E. Levine, Benjamin C. Trumble, Hillard Kaplan, Hooman Allayee, Beate R. Ritz, Brian Chen, Ake T. Lu, Tammy M. Rickabaugh, Beth D. Jamieson, Dianjianyi Sun, Shengxu Li, Wei Chen, Lluis Quintana-Murci, Maud Fagny…

    Genome Biology 2016 17:171

    Published on: 11 August 2016

  13. Research

    Epigenetic assimilation in the aging human brain

    Epigenetic drift progressively increases variation in DNA modification profiles of aging cells, but the finale of such divergence remains elusive. In this study, we explored the dynamics of DNA modification an...

    Gabriel Oh, Sasha Ebrahimi, Sun-Chong Wang, Rene Cortese, Zachary A. Kaminsky, Irving I. Gottesman, James R. Burke, Brenda L. Plassman and Art Petronis

    Genome Biology 2016 17:76

    Published on: 28 April 2016

  14. Research

    Systematic identification of genetic influences on methylation across the human life course

    The influence of genetic variation on complex diseases is potentially mediated through a range of highly dynamic epigenetic processes exhibiting temporal variation during development and later life. Here we pr...

    Tom R. Gaunt, Hashem A. Shihab, Gibran Hemani, Josine L. Min, Geoff Woodward, Oliver Lyttleton, Jie Zheng, Aparna Duggirala, Wendy L. McArdle, Karen Ho, Susan M. Ring, David M. Evans, George Davey Smith and Caroline L. Relton

    Genome Biology 2016 17:61

    Published on: 31 March 2016

  15. Research Highlight

    External signals shape the epigenome

    A new study shows how a single cytokine, interleukin-4, regulates hematopoietic lineage choice by activating the JAK3–STAT6 pathway, which causes dendritic-cell-specific DNA demethylation.

    Andreas Lennartsson

    Genome Biology 2016 17:18

    Published on: 1 February 2016

  16. Research

    Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer

    One of the hallmarks of cancer is the disruption of gene expression patterns. Many molecular lesions contribute to this phenotype, and the importance of aberrant DNA methylation profiles is increasingly recogn...

    Holger Heyn, Enrique Vidal, Humberto J. Ferreira, Miguel Vizoso, Sergi Sayols, Antonio Gomez, Sebastian Moran, Raquel Boque-Sastre, Sonia Guil, Anna Martinez-Cardus, Charles Y. Lin, Romina Royo, Jose V. Sanchez-Mut, Ramon Martinez, Marta Gut, David Torrents…

    Genome Biology 2016 17:11

    Published on: 26 January 2016

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