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Differential Methylation Analysis with Next-Generation Sequencing

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Next Generation Sequencing in Cancer Research, Volume 2

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Abstract

DNA methylation is an important epigenetic modification of DNA sequences, which could potentially affect gene expression and final phenotypes. Abnormal methylation has been discovered in many types of cancers and other human diseases. Detecting differentially methylated loci (DML) and differentially methylated regions (DMRs) is critical in understanding the genetic mechanism of cancer and identifying biomarkers and treatment targets, which could be used for cancer diagnosis, prognosis, prevention, and treatment. Next-generation sequencing (NGS) has been widely used to generate genome-wide methylation data. These data provide unique challenges in the differential methylation analysis at genomic levels. In this paper, we discuss these challenges and some statistical and computational approaches for detecting DML and DMRs for NGS methylation data.

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Author information

Authors and Affiliations

  1. Department of Biostatistics and Epidemiology, Medical College of Georgia, Georgia Regents University, Augusta, GA, 30912, USA

    Hongyan Xu Ph.D.

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  1. Hongyan Xu Ph.D.
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Correspondence to Hongyan Xu Ph.D. .

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Editors and Affiliations

  1. Department of Pathology and Laboratory, Medicine, Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada

    Wei Wu

  2. Faculty of Science, Biochemistry Department, Center of Innovation in Personalized Medicine, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia

    Hani Choudhry

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Xu, H. (2015). Differential Methylation Analysis with Next-Generation Sequencing. In: Wu, W., Choudhry, H. (eds) Next Generation Sequencing in Cancer Research, Volume 2. Springer, Cham. https://doi.org/10.1007/978-3-319-15811-2_14

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