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 P. Nephew

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapter

12 Scopus citations

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
Subtitle of host publicationRisk Assessment, Diagnosis, Treatment, and Prognosis
PublisherSpringer New York
Pages653-675
Number of pages23
ISBN (Electronic)9781493918041
ISBN (Print)9781493918034
DOIs
StatePublished - Nov 24 2014

Keywords

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

ASJC Scopus subject areas

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

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