Global DNA methylation profiling technologies and the ovarian cancer methylome

Jessica Tang, Fang Fang, Dave F. Miller, Jay M. Pilrose, Daniela Matei, Tim Hui Ming Huang, Kenneth Nephew

Research output: Chapter in Book/Report/Conference proceedingChapter

11 Citations (Scopus)

Abstract

Cytosine methylation in DNA constitutes an important epigenetic layer of transcriptional and regulatory control in many eukaryotes. Profiling DNA methylation across the genome is critical to understanding the influence of epigenetics in normal biology and disease, such as cancer. Genome-wide analyses such as arrays and next-generation sequencing (NGS) technologies have been used to assess large fractions of the methylome at a single-base-pair resolution. However, the range of DNA methylation profiling techniques can make selecting the appropriate protocol a challenge. This chapter discusses the advantages and disadvantages of various methylome detection approaches to assess which is appropriate for the question at hand. Here, we focus on four prominent genome-wide approaches: whole-genome bisulfite sequencing (WGBS); methyl-binding domain capture sequencing (MBDCap-Seq); reduced-representation-bisulfite-sequencing (RRBS); and Infinium Methylation450 BeadChips (450 K, Illumina). We discuss some of the requirements, merits, and challenges that should be considered when choosing a methylome technology to ensure that it will be informative. In addition, we show how genome-wide methylation detection arrays and high- throughput sequencing have provided immense insight into ovarian cancer-specific methylation signatures that may serve as diagnostic biomarkers or predict patient response to epigenetic therapy.

Original languageEnglish (US)
Title of host publicationCancer Epigenetics: Risk Assessment, Diagnosis, Treatment, and Prognosis
PublisherSpringer New York
Pages653-675
Number of pages23
ISBN (Print)9781493918041, 9781493918034
DOIs
StatePublished - Nov 24 2014

Fingerprint

DNA Fingerprinting
DNA Methylation
Ovarian Neoplasms
Genes
Methylation
Genome
Technology
Epigenomics
Cytosine
Biomarkers
Eukaryota
Base Pairing
Hand
Throughput
DNA
Neoplasms

Keywords

  • Epigenetics
  • Methylation
  • Next-generation sequencing
  • Ovarian cancer
  • Whole-genome bisulfite sequencing

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Tang, J., Fang, F., Miller, D. F., Pilrose, J. M., Matei, D., Huang, T. H. M., & Nephew, K. (2014). Global DNA methylation profiling technologies and the ovarian cancer methylome. In Cancer Epigenetics: Risk Assessment, Diagnosis, Treatment, and Prognosis (pp. 653-675). Springer New York. https://doi.org/10.1007/978-1-4939-1804-1_34

Global DNA methylation profiling technologies and the ovarian cancer methylome. / Tang, Jessica; Fang, Fang; Miller, Dave F.; Pilrose, Jay M.; Matei, Daniela; Huang, Tim Hui Ming; Nephew, Kenneth.

Cancer Epigenetics: Risk Assessment, Diagnosis, Treatment, and Prognosis. Springer New York, 2014. p. 653-675.

Research output: Chapter in Book/Report/Conference proceedingChapter

Tang, J, Fang, F, Miller, DF, Pilrose, JM, Matei, D, Huang, THM & Nephew, K 2014, Global DNA methylation profiling technologies and the ovarian cancer methylome. in Cancer Epigenetics: Risk Assessment, Diagnosis, Treatment, and Prognosis. Springer New York, pp. 653-675. https://doi.org/10.1007/978-1-4939-1804-1_34
Tang J, Fang F, Miller DF, Pilrose JM, Matei D, Huang THM et al. Global DNA methylation profiling technologies and the ovarian cancer methylome. In Cancer Epigenetics: Risk Assessment, Diagnosis, Treatment, and Prognosis. Springer New York. 2014. p. 653-675 https://doi.org/10.1007/978-1-4939-1804-1_34
Tang, Jessica ; Fang, Fang ; Miller, Dave F. ; Pilrose, Jay M. ; Matei, Daniela ; Huang, Tim Hui Ming ; Nephew, Kenneth. / Global DNA methylation profiling technologies and the ovarian cancer methylome. Cancer Epigenetics: Risk Assessment, Diagnosis, Treatment, and Prognosis. Springer New York, 2014. pp. 653-675
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