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Updated: Oct 5, 2025
Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies
Published on: May 6, 2022
GMQN: A Reference-Based Method for Correcting Batch Effects and Probe Bias in HumanMethylation BeadChip
Zhuang Xiong1,2,3, Mengwei Li1,2,3, Yingke Ma1,2
1National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China.
Abstract:
The Illumina HumanMethylation BeadChip is one of the most cost-effective methods to quantify DNA methylation levels at single-base resolution across the human genome, which makes it a routine platform for epigenome-wide association studies. It has accumulated tens of thousands of DNA methylation array samples in public databases, providing great support for data integration and further analysis. However, the majority of public DNA methylation data are deposited as processed data without background probes which are widely used in data normalization. Here, we present Gaussian mixture quantile normalization (GMQN), a reference based method for correcting batch effects as well as probe bias in the HumanMethylation BeadChip. Availability and implementation: https://github.com/MengweiLi-project/gmqn.
