Base resolution methylome profiling: Considerations in platform selection, data preprocessing and analysis

Research output: Contribution to journalReview article

42 Scopus citations

Abstract

Bisulfite treatment-based methylation microarray (mainly Illumina 450K Infinium array) and next-generation sequencing (reduced representation bisulfite sequencing, Agilent SureSelect Human Methyl-Seq, NimbleGen SeqCap Epi CpGiant or whole-genome bisulfite sequencing) are commonly used for base resolution DNA methylome research. Although multiple tools and methods have been developed and used for the data preprocessing and analysis, confusions remains for these platforms including how and whether the 450k array should be normalized; which platform should be used to better fit researchers' needs; and which statistical models would be more appropriate for differential methylation analysis. This review presents the commonly used platforms and compares the pros and cons of each in methylome profiling. We then discuss approaches to study design, data normalization, bias correction and model selection for differentially methylated individual CpGs and regions.

Original languageEnglish (US)
Pages (from-to)813-828
Number of pages16
JournalEpigenomics
Volume7
Issue number5
DOIs
StatePublished - Aug 2015

Keywords

  • DNA methylation
  • bisulfite sequencing
  • differential methylation
  • methylation 450K array
  • normalization
  • reduced representation bisulfite sequencing
  • study design

ASJC Scopus subject areas

  • Genetics
  • Cancer Research

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