Ultra-Deep Sequencing of Bisulfite-Modified DNA

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

doi:10.1016/B978-0-12-800140-0.00003-0

Ultra-Deep Sequencing of Bisulfite-Modified DNA

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

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Abstract

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 language	English (US)
Title of host publication	Epigenomics in Health and Disease
Publisher	Elsevier Inc.
Pages	47-72
Number of pages	26
ISBN (Electronic)	9780128004968
ISBN (Print)	9780128001400
DOIs	https://doi.org/10.1016/B978-0-12-800140-0.00003-0
State	Published - 2016
Externally published	Yes

Keywords

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)

Access to Document

10.1016/B978-0-12-800140-0.00003-0

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abstract = "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.",

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