RELIC: a novel dye-bias correction method for Illumina Methylation BeadChip

BMC Genomics

Methodology Article

Liang Niu¹  Sabine A. S. Langie²  Patrick De Boever²  Zongli Xu³  Jack A. Taylor⁴ 

[1] Division of Biostatistics and Bioinformatics, Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH, USA;Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium;Faculty of Sciences, Hasselt University, Diepenbeek, Belgium;Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA;Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA;Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA;

关键词: RELIC;    DNA methylation;    Dye-bias correction;    Illumina HumanMethylation450;    Illumina MethylationEPIC;    Data preprocessing;   

DOI  :  10.1186/s12864-016-3426-3

 received in 2016-07-23, accepted in 2016-12-15,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsHere 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).ConclusionsRELIC 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.

【 授权许可】

CC BY   
© The Author(s). 2017

【 图 表 】

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