A comprehensive overview of Infinium HumanMethylation450 data processing

Infinium HumanMethylation450 beadarray is a popular technology to explore DNA methylomes in health and disease, and there is a current explosion in the use of this technique. Despite experience acquired from gene expression microarrays, analyzing Infinium Methylation arrays appeared more complex tha...

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Bibliographic Details
Published in:Briefings in bioinformatics Vol. 15; no. 6; pp. 929 - 941
Main Authors: Dedeurwaerder, S., Defrance, M., Bizet, M., Calonne, E., Bontempi, G., Fuks, F.
Format: Journal Article
Language:English
Published: England Oxford Publishing Limited (England) 01.11.2014
Oxford University Press
Subjects:
Bioinformatics
Biotechnology
Computational Biology
CpG Islands
Data analysis
Data interpretation
Data Interpretation, Statistical
Data processing
DNA Methylation
Gene expression
Genome, Human
Humans
Oligonucleotide Array Sequence Analysis - statistics & numerical data
Oligonucleotide Probes
Polymorphism, Single Nucleotide
Software
Genome-wide DNA methylation technology
Epigenomics
ISSN:1467-5463, 1477-4054, 1477-4054
Online Access:Get full text
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Summary:Infinium HumanMethylation450 beadarray is a popular technology to explore DNA methylomes in health and disease, and there is a current explosion in the use of this technique. Despite experience acquired from gene expression microarrays, analyzing Infinium Methylation arrays appeared more complex than initially thought and several difficulties have been encountered, as those arrays display specific features that need to be taken into consideration during data processing. Here, we review several issues that have been highlighted by the scientific community, and we present an overview of the general data processing scheme and an evaluation of the different normalization methods available to date to guide the 450K users in their analysis and data interpretation.
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These authors contributed equally to this work.
ISSN:1467-5463
1477-4054
1477-4054
DOI:10.1093/bib/bbt054