Ultra-Deep Sequencing of Bisulfite-Modified DNA

Tingting Qin, Yongseok Park, Maria E. Figueroa, Maureen A. Sartor

Research output: Chapter in Book/Report/Conference proceedingChapter


Ultra-deep sequencing of bisulfite-modified DNA is considered the gold standard method for assessment of DNA methylation across the genome. In this chapter, an introduction to whole-genome bisulfite sequencing and reduced representation bisulfite sequencing are presented, as well as their advantages and disadvantages. Specific topics include (i) sample preparation and study design; (ii) quality controls and other technical considerations for ultra-deep sequencing; (iii) testing methods for differentially methylated sites or regions, focusing on the beta-binomial model; (iv) annotation, visualization, and post hoc tests of results; and (v) experimental extensions to bisulfite sequencing. Specific applications of bisulfite sequencing to cancers, such as leukemia, and their findings are also presented.

Original languageEnglish (US)
Title of host publicationEpigenomics in Health and Disease
PublisherElsevier Inc.
Number of pages26
ISBN (Electronic)9780128004968
ISBN (Print)9780128001400
StatePublished - 2016
Externally publishedYes


  • Beta-binomial model
  • CpG islands
  • DNA methylation
  • Differentially methylated regions
  • Reduced representation bisulfite sequencing
  • Sodium bisulfite
  • Whole-genome bisulfite sequencing

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)


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