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: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Cytosine methylation in DNA constitutes an important epigenetic layer of transcriptional and regulatory control in many eukaryotes. Profi ling DNA methylation across the genome is critical to understanding the infl uence 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 profi ling 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 bisulfi te sequencing (WGBS); methyl-binding domain capture sequencing (MBDCap-Seq); reduced-representation-bisulfi te-sequencing (RRBS); and Infi nium 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-specifi c methylation signatures that may serve as diagnostic biomarkers or predict patient response to epigenetic therapy.

Original languageEnglish
Pages (from-to)653-675
Number of pages23
JournalMethods in molecular biology (Clifton, N.J.)
Volume1238
DOIs
StatePublished - 2015
Externally publishedYes

Fingerprint

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

Keywords

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

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

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.

In: Methods in molecular biology (Clifton, N.J.), Vol. 1238, 2015, p. 653-675.

Research output: Contribution to journalArticle

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. In: Methods in molecular biology (Clifton, N.J.). 2015 ; Vol. 1238. pp. 653-675.
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