Low-level processing of Illumina Infinium DNA Methylation BeadArrays

By Timothy Triche, D. Weisenberger, D. J. Van Den Berg, Peter W. Laird, K. Siegmund. Nucleic Acids Research, 2013

794 citations recorded by the source corpus.

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.

Subfields: Health, Toxicology and Mutagenesis, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/76550192bddbafb5e05d939ede2b69e1b00428b2

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In Health, Toxicology and Mutagenesis

In Molecular Biology

Citations in the corpus

ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip (2015, methodology): “using ‘out-of-band’ signal intensities for Infinium I probes followed by adjustment using normal-exponential (noob) or gamma convolution (goob) methods (6).”
Functional normalization of 450k methylation array data improves replication in large cancer studies (2014, methodology): “These metrics include assessing variability between technical replicates [13,14,16,17,46], and comparing methylation levels to an external gold standard measurement, such as bisulfite sequencing [11,14,17].”
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Oncogenic Signaling Pathways in The Cancer Genome Atlas (2018, background): “…Level 1 IDAT ﬁles to calculate out-of-band (‘oob’) probe intensities as a surrogate for background intensity, superior to internal negative controls (Triche et al., 2013). cg13601799 is a Type I probe with both methylated (M) and unmethylated (U) versions in the red color channel, and therefore…”
Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes (2016, methodology): “We performed noob background correction (19) and dye bias correction following the TCGA data processing pipeline (4).”
Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells (2016, neutral): “0) Monlong et al., 2014 https://github.com/jmonlong/sQTLseekeR AStalavista 3.2 Foissac and Sammeth, 2007; Monlong et al., 2014 http://sammeth.net/confluence/display/ASTA/2+-+Download Minfi Aryee et al., 2014 https://bioconductor.org/packages/release/bioc/html/minfi.html NOOB Triche et al., 2013 http”
SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions (2018, methodology): “For each TCGA sample, we first performed background subtraction and dye bias correction across the entire array with methylumi (21), which was the method referenced in TCGA projects (2).”
Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi (2016, methodology): “…(Maksimovic, Gordon, and Oshlack, 2012), stratiﬁed quantile normalization as discussed in Touleimat and Tost (2012) and Aryee et al. (2014), single-sample noob background correction followed by dye bias correction (Triche et al., 2013), and functional normalization (Fortin, Labbe, et al., 2014).”
Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. (2017, positive): “Background correction was performed via normal-exponential deconvolution (Triche et al., 2013).”