Evaluating the Consistency of Gene Methylation in Liver Cancer Using Bisulfite Sequencing Data

Xubin Zheng; Qiong Wu; Haonan Wu; Kwong-Sak Leung; Man-Hon Wong; Xueyan Liu; Lixin Cheng

doi:10.3389/fcell.2021.671302

Evaluating the Consistency of Gene Methylation in Liver Cancer Using Bisulfite Sequencing Data

Front Cell Dev Biol. 2021 Apr 29:9:671302. doi: 10.3389/fcell.2021.671302. eCollection 2021.

Authors

Xubin Zheng^{1

2}, Qiong Wu^{1

3}, Haonan Wu¹, Kwong-Sak Leung², Man-Hon Wong², Xueyan Liu¹, Lixin Cheng¹

Affiliations

¹ Department of Critical Medicine, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen, China.
² Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China.
³ School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.

Abstract

Bisulfite sequencing is considered as the gold standard approach for measuring DNA methylation, which acts as a pivotal part in regulating a variety of biological processes without changes in DNA sequences. In this study, we introduced the most prevalent methods for processing bisulfite sequencing data and evaluated the consistency of the data acquired from different measurements in liver cancer. Firstly, we introduced three commonly used bisulfite sequencing assays, i.e., reduced-representation bisulfite sequencing (RRBS), whole-genome bisulfite sequencing (WGBS), and targeted bisulfite sequencing (targeted BS). Next, we discussed the principles and compared different methods for alignment, quality assessment, methylation level scoring, and differentially methylated region identification. After that, we screened differential methylated genes in liver cancer through the three bisulfite sequencing assays and evaluated the consistency of their results. Ultimately, we compared bisulfite sequencing to 450 k beadchip and assessed the statistical similarity and functional association of differentially methylated genes (DMGs) among the four assays. Our results demonstrated that the DMGs measured by WGBS, RRBS, targeted BS and 450 k beadchip are consistently hypo-methylated in liver cancer with high functional similarity.

Keywords: DNA methylation; liver cancer; reduced-representation bisulfite sequencing; targeted bisulfite sequencing; whole-genome bisulfite sequencing.