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Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/23285

Title: RELIC: a novel dye-bias correction method for Illumina Methylation BeadChip
Authors: Xu, Zongli
Langie, Sabine A. S.
De Boever, Patrick
Taylor, Jack A.
Niu, Liang
Issue Date: 2017
Citation: BMC GENOMICS, 18 (Art N° 4)
Abstract: Background: The Illumina Infinium HumanMethylation450 BeadChip and its successor, Infinium MethylationEPIC BeadChip, have been extensively utilized in epigenome-wide association studies. Both arrays use two fluorescent dyes (Cy3-green/Cy5-red) to measure methylation level at CpG sites. However, performance difference between dyes can result in biased estimates of methylation levels. Results: Here we describe a novel method, called REgression on Logarithm of Internal Control probes (RELIC) to correct for dye bias on whole array by utilizing the intensity values of paired internal control probes that monitor the two color channels. We evaluate the method in several datasets against other widely used dye-bias correction methods. Results on data quality improvement showed that RELIC correction statistically significantly outperforms alternative dye-bias correction methods. We incorporated the method into the R package ENmix, which is freely available from the Bioconductor website(https://www.bioconductor.org/packages/release/bioc/html/ENmix.html). Conclusions: RELIC is an efficient and robust method to correct for dye-bias in Illumina Methylation BeadChip data. It outperforms other alternative methods and conveniently implemented in R package ENmix to facilitate DNA methylation studies.
Notes: [Xu, Zongli; Taylor, Jack A.] Natl Inst Environm Hlth Sci, Epidemiol Branch, NIH, Res Triangle Pk, NC USA. [Langie, Sabine A. S.; De Boever, Patrick] Flemish Inst Technol Res VITO, Environm Risk & Hlth Unit, Mol, Belgium. [Langie, Sabine A. S.; De Boever, Patrick] Hasselt Univ, Fac Sci, Diepenbeek, Belgium. [Taylor, Jack A.] Natl Inst Environm Hlth Sci, Epigenet & Stem Cell Biol Lab, NIH, Res Triangle Pk, NC USA. [Niu, Liang] Univ Cincinnati, Coll Med, Dept Environm Hlth, Div Biostat & Bioinformat, Cincinnati, OH 45267 USA.
URI: http://hdl.handle.net/1942/23285
DOI: 10.1186/s12864-016-3426-3
ISI #: 000391332000004
ISSN: 1471-2164
Category: A1
Type: Journal Contribution
Appears in Collections: Research publications

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