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) |
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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 | |
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)