A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data

Ting Wang, Weihua Guan, Jerome Lin, Nadia Boutaoui, Glorisa Canino, Jianhua Luo, Juan Carlos Celedón, Wei Chen

Research output: Contribution to journalArticlepeer-review

25 Scopus citations

Abstract

DNA methylation plays an important role in disease etiology. The Illumina Infinium HumanMethylation450 (450K) BeadChip is a widely used platform in large-scale epidemiologic studies. This platform can efficiently and simultaneously measure methylation levels at ∼480,000 CpG sites in the human genome in multiple study samples. Due to the intrinsic chip design of 2 types of chemistry probes, data normalization or preprocessing is a critical step to consider before data analysis. To date, numerous methods and pipelines have been developed for this purpose, and some studies have been conducted to evaluate different methods. However, validation studies have often been limited to a small number of CpG sites to reduce the variability in technical replicates. In this study, we measured methylation on a set of samples using both whole-genome bisulfite sequencing (WGBS) and 450K chips. We used WGBS data as a gold standard of true methylation states in cells to compare the performances of 8 normalization methods for 450K data on a genome-wide scale. Analyses on our dataset indicate that the most effective methods are peak-based correction (PBC) and quantile normalization plus β-mixture quantile normalization (QN.BMIQ). To our knowledge, this is the first study to systematically compare existing normalization methods for Illumina 450K data using novel WGBS data. Our results provide a benchmark reference for the analysis of DNA methylation chip data, particularly in white blood cells.

Original languageEnglish (US)
Pages (from-to)662-669
Number of pages8
JournalEpigenetics
Volume10
Issue number7
DOIs
StatePublished - Jan 1 2015

Bibliographical note

Funding Information:
This study was supported by the Competitive Medical Research Fund (WC) from the University of Pittsburgh, and by grants HL07996 and HL117191 (JCC) from the US. National Institutes of Health.

Keywords

  • DNA methylation
  • Epigenetics
  • Illumina 450K
  • Microarray
  • Normalization
  • Whole-genome bisulfite sequencing (WGBS)

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