A Guide to Illumina BeadChip Data Analysis

  • Michael C. Wu
  • Pei-Fen Kuan
Part of the Methods in Molecular Biology book series (MIMB, volume 1708)


The Illumina Infinium BeadChips are a powerful array-based platform for genome-wide DNA methylation profiling at approximately 485,000 (450K) and 850,000 (EPIC) CpG sites across the genome. The platform is used in many large-scale population-based epigenetic studies of complex diseases, environmental exposures, or other experimental conditions. This chapter provides an overview of the key steps in analyzing Illumina BeadChip data. We describe key preprocessing steps including data extraction and quality control as well as normalization strategies. We further present principles and guidelines for conducting association analysis at the individual CpG level as well as more sophisticated pathway-based association tests.

Key words

DNA methylation Epigenome-wide association studies Hypothesis testing Normalization Pathway analysis Quality control 


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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  1. 1.Public Health Sciences DivisionFred Hutchinson Cancer Research CenterSeattleUSA
  2. 2.Department of Applied Mathematics and StatisticsStony Brook UniversityStony BrookUSA

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