Low-level processing of Illumina Infinium DNA Methylation BeadArrays

We propose a novel approach to background correction for Infinium HumanMethylation data to account for technical variation in background fluorescence signal. Our approach capitalizes on a new use for the Infinium I design bead types to measure non-specific fluorescence in the colour channel opposite...

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Bibliographic Details
Published in:Nucleic acids research Vol. 41; no. 7; p. e90
Main Authors: Triche, Timothy J., Weisenberger, Daniel J., Van Den Berg, David, Laird, Peter W., Siegmund, Kimberly D.
Format: Journal Article
Language:English
Published: England Oxford University Press 01.04.2013
Subjects:
DNA Methylation
Fluorescent Dyes
HapMap Project
Humans
Methods Online
Oligonucleotide Array Sequence Analysis - methods
ISSN:0305-1048, 1362-4962, 1362-4962
Online Access:Get full text
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Summary:We propose a novel approach to background correction for Infinium HumanMethylation data to account for technical variation in background fluorescence signal. Our approach capitalizes on a new use for the Infinium I design bead types to measure non-specific fluorescence in the colour channel opposite of their design (Cy3/Cy5). This provides tens of thousands of features for measuring background instead of the much smaller number of negative control probes on the platforms (n = 32 for HumanMethylation27 and n = 614 for HumanMethylation450, respectively). We compare the performance of our methods with existing approaches, using technical replicates of both mixture samples and biological samples, and demonstrate that within- and between-platform artefacts can be substantially reduced, with concomitant improvement in sensitivity, by the proposed methods.
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ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkt090