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 | |
| State | Published - Oct 28 2015 |
| Externally published | Yes |
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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
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 proceeding › Chapter
}
TY - CHAP
T1 - Ultra-Deep Sequencing of Bisulfite-Modified DNA
AU - Qin, Tingting
AU - Park, Yongseok
AU - Figueroa, Maria
AU - Sartor, Maureen A.
PY - 2015/10/28
Y1 - 2015/10/28
N2 - 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.
AB - 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.
KW - Beta-binomial model
KW - CpG islands
KW - Differentially methylated regions
KW - DNA methylation
KW - Reduced representation bisulfite sequencing
KW - Sodium bisulfite
KW - Whole-genome bisulfite sequencing
UR - http://www.scopus.com/inward/record.url?scp=84980315333&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84980315333&partnerID=8YFLogxK
U2 - 10.1016/B978-0-12-800140-0.00003-0
DO - 10.1016/B978-0-12-800140-0.00003-0
M3 - Chapter
AN - SCOPUS:84980315333
SN - 9780128001400
SP - 47
EP - 72
BT - Epigenomics in Health and Disease
PB - Elsevier Inc.
ER -