GMQN: A Reference-Based Method for Correcting Batch Effects and Probe Bias in HumanMethylation BeadChip

Zhuang Xiong; Zhuang Xiong; Zhuang Xiong; Mengwei Li; Mengwei Li; Mengwei Li; Yingke Ma; Yingke Ma; Rujiao Li; Rujiao Li; Yiming Bao; Yiming Bao; Yiming Bao

doi:10.3389/fgene.2021.810985

Frontiers in Genetics (Jan 2022)

GMQN: A Reference-Based Method for Correcting Batch Effects and Probe Bias in HumanMethylation BeadChip

Zhuang Xiong,
Zhuang Xiong,
Zhuang Xiong,
Mengwei Li,
Mengwei Li,
Mengwei Li,
Yingke Ma,
Yingke Ma,
Rujiao Li,
Rujiao Li,
Yiming Bao,
Yiming Bao,
Yiming Bao

Affiliations

Zhuang Xiong: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
Zhuang Xiong: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
Zhuang Xiong: University of Chinese Academy of Sciences, Beijing, China
Mengwei Li: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
Mengwei Li: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
Mengwei Li: University of Chinese Academy of Sciences, Beijing, China
Yingke Ma: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
Yingke Ma: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
Rujiao Li: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
Rujiao Li: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
Yiming Bao: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
Yiming Bao: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
Yiming Bao: University of Chinese Academy of Sciences, Beijing, China

DOI: https://doi.org/10.3389/fgene.2021.810985
Journal volume & issue: Vol. 12

Abstract

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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.

Published in Frontiers in Genetics

ISSN: 1664-8021 (Online)
Publisher: Frontiers Media S.A.
Country of publisher: Switzerland
LCC subjects: Science: Biology (General): Genetics
Website: http://journal.frontiersin.org/journal/genetics

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Abstract

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