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

Zheng, Xubin1,2; Wu, Qiong1,3; Wu, Haonan1; Leung, Kwong-Sak2; Wong, Man-Hon2; Liu, Xueyan1; Cheng, Lixin1

2021-04-29

10.3389/fcell.2021.671302

Frontiers in Cell and Developmental Biology   影响因子和分区

2296-634X

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.

whole-genome bisulfite sequencing reduced-representation bisulfite sequencing targeted bisulfite sequencing liver cancer DNA methylation

SCI

英语

第一 ; 通讯

Guangdong Basic and Applied Basic Research Foundation[2019A1515110097] ; Shenzhen Key Laboratory of Prevention and Treatment of Severe Infections[ZDSYS20200811142804014]

Cell Biology ; Developmental Biology

Cell Biology ; Developmental Biology

WOS:000649660100001

FRONTIERS MEDIA SA

Web of Science

1.Jinan Univ, Southern Univ Sci & Technol, Shenzhen Peoples Hosp, Affiliated Hosp 1,Dept Crit Med,Clin Med Coll 2, Shenzhen, Peoples R China
2.Chinese Univ Hong Kong, Dept Comp Sci & Engn, Hong Kong, Peoples R China
3.Chinese Univ Hong Kong, Sch Biomed Sci, Hong Kong, Peoples R China

Zheng, Xubin,Wu, Qiong,Wu, Haonan,et al. Evaluating the Consistency of Gene Methylation in Liver Cancer Using Bisulfite Sequencing Data[J]. Frontiers in Cell and Developmental Biology,2021,9.

Zheng, Xubin.,Wu, Qiong.,Wu, Haonan.,Leung, Kwong-Sak.,Wong, Man-Hon.,...&Cheng, Lixin.(2021).Evaluating the Consistency of Gene Methylation in Liver Cancer Using Bisulfite Sequencing Data.Frontiers in Cell and Developmental Biology,9.

Zheng, Xubin,et al."Evaluating the Consistency of Gene Methylation in Liver Cancer Using Bisulfite Sequencing Data".Frontiers in Cell and Developmental Biology 9(2021).