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Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies
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A comprehensive overview of Infinium HumanMethylation450 data processing.

Sarah Dedeurwaerder, Matthieu Defrance, Martin Bizet

    Briefings in Bioinformatics
    |August 31, 2013
    PubMed
    Summary

    The Infinium HumanMethylation450 beadarray is widely used for DNA methylome analysis. This review addresses data processing challenges and evaluates normalization methods for the 450K array to aid researchers.

    Keywords:
    EpigenomicsGenome-wide DNA methylation technology

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    Area of Science:

    • Epigenetics and Genomics
    • Bioinformatics and Computational Biology

    Background:

    • The Infinium HumanMethylation450 beadarray is a prevalent tool for studying DNA methylomes in various biological contexts.
    • Analysis of Infinium Methylation arrays presents unique challenges compared to gene expression microarrays, requiring specialized data processing strategies.

    Purpose of the Study:

    • To review common issues encountered in Infinium HumanMethylation450 beadarray data processing.
    • To provide an overview of general data processing schemes for the 450K array.
    • To evaluate available normalization methods to assist users in data analysis and interpretation.

    Main Methods:

    • Literature review of scientific community-highlighted issues in 450K array analysis.
    • Overview of standard data processing workflows for methylation array data.
    • Comparative evaluation of different normalization techniques applicable to 450K data.

    Main Results:

    • Identified specific challenges in processing Infinium Methylation 450K array data.
    • Presented a general framework for handling 450K array data.
    • Assessed the performance and suitability of various normalization methods.

    Conclusions:

    • Effective data processing and normalization are crucial for accurate DNA methylome analysis using the 450K array.
    • This review offers guidance to researchers for optimizing their analysis and interpretation of 450K array data.
    • Addressing the complexities of 450K array data processing enhances the utility of this technology in health and disease research.