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A Guide to Illumina BeadChip Data Analysis

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DNA Methylation Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1708))

Abstract

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.

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Author information

Authors and Affiliations

  1. Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, M3-C102, Seattle, WA, 98109, USA

    Michael C. Wu

  2. Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA

    Pei-Fen Kuan

Authors
  1. Michael C. Wu
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  2. Pei-Fen Kuan
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Corresponding author

Correspondence to Michael C. Wu .

Editor information

Editors and Affiliations

  1. Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA—Institut de Biologie Francois Jacob, Evry, France

    Jörg Tost

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Wu, M.C., Kuan, PF. (2018). A Guide to Illumina BeadChip Data Analysis. In: Tost, J. (eds) DNA Methylation Protocols. Methods in Molecular Biology, vol 1708. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7481-8_16

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  • DOI: https://doi.org/10.1007/978-1-4939-7481-8_16

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7479-5

  • Online ISBN: 978-1-4939-7481-8

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