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

• DOI: 10.3389/fcell.2021.671302
• Publication Date: 2021-04-29T05:28:21Z
• Authors: Xubin Zheng; Qiong Wu; Haonan Wu; Kwong-Sak Leung; Man-Hon Wong; Xueyan Liu; Lixin Cheng
• Keywords: Bisulfite; Bisulfite sequencing; Illumina Methylation Assay

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