Low-level processing of Illumina Infinium DNA Methylation BeadArrays

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ID: 304406
2013
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Abstract
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.
Reference Key
openalex_W2081182312 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Timothy J. Triche, Daniel J. Weisenberger, David Van Den Berg, Peter W. Laird, Kimberly D. Siegmund
Journal Nucleic Acids Research
Year 2013
DOI
10.1093/nar/gkt090
URL
https://academic.oup.com/nar/article-pdf/41/7/e90/25341449/gkt090.pdf
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