Differential methylation analysis with next-generation sequencing

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

DNA methylation is an important epigenetic modification of DNAsequences, which could potentially affect gene expression and final phenotypes. Abnormal methylation has been discovered in manytypes 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.

Original languageEnglish (US)
Title of host publicationNext Generation Sequencing in Cancer Research, Volume 2
Subtitle of host publicationFrom Basepairs to Bedsides
PublisherSpringer International Publishing
Pages229-238
Number of pages10
ISBN (Electronic)9783319158112
ISBN (Print)9783319158105
DOIs
StatePublished - Jan 1 2015

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Keywords

  • DNA methylation
  • Differential methylation
  • Epigenetic association
  • Epigenetic marker
  • Next-generation sequencing

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Xu, H. (2015). Differential methylation analysis with next-generation sequencing. In Next Generation Sequencing in Cancer Research, Volume 2: From Basepairs to Bedsides (pp. 229-238). Springer International Publishing. https://doi.org/10.1007/978-3-319-15811-2_14