Ultra-Deep Sequencing of Bisulfite-Modified DNA

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

Research output: Chapter in Book/Report/Conference proceedingChapter

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 languageEnglish (US)
Title of host publicationEpigenomics in Health and Disease
PublisherElsevier Inc.
Pages47-72
Number of pages26
ISBN (Electronic)9780128004968
ISBN (Print)9780128001400
DOIs
StatePublished - Oct 28 2015
Externally publishedYes

Fingerprint

High-Throughput Nucleotide Sequencing
DNA
Genes
Genome
Statistical Models
DNA Methylation
Quality Control
Quality control
Leukemia
Visualization
hydrogen sulfite
Testing
Neoplasms

Keywords

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

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Qin, T., Park, Y., Figueroa, M., & Sartor, M. A. (2015). Ultra-Deep Sequencing of Bisulfite-Modified DNA. In Epigenomics in Health and Disease (pp. 47-72). Elsevier Inc.. https://doi.org/10.1016/B978-0-12-800140-0.00003-0

Ultra-Deep Sequencing of Bisulfite-Modified DNA. / Qin, Tingting; Park, Yongseok; Figueroa, Maria; Sartor, Maureen A.

Epigenomics in Health and Disease. Elsevier Inc., 2015. p. 47-72.

Research output: Chapter in Book/Report/Conference proceedingChapter

Qin, T, Park, Y, Figueroa, M & Sartor, MA 2015, Ultra-Deep Sequencing of Bisulfite-Modified DNA. in Epigenomics in Health and Disease. Elsevier Inc., pp. 47-72. https://doi.org/10.1016/B978-0-12-800140-0.00003-0
Qin T, Park Y, Figueroa M, Sartor MA. Ultra-Deep Sequencing of Bisulfite-Modified DNA. In Epigenomics in Health and Disease. Elsevier Inc. 2015. p. 47-72 https://doi.org/10.1016/B978-0-12-800140-0.00003-0
Qin, Tingting ; Park, Yongseok ; Figueroa, Maria ; Sartor, Maureen A. / Ultra-Deep Sequencing of Bisulfite-Modified DNA. Epigenomics in Health and Disease. Elsevier Inc., 2015. pp. 47-72
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