Analysis and Performance Assessment of the Whole Genome Bisulfite Sequencing Data Workflow: Currently Available Tools and a Practical Guide to Advance DNA Methylation Studies
Ting Gong
Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813 USA
Search for more papers by this authorHeather Borgard
Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813 USA
Search for more papers by this authorZao Zhang
Department of Medicine, The Queen's Medical Center, Honolulu, HI, 96813 USA
Search for more papers by this authorShaoqiu Chen
Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813 USA
Search for more papers by this authorZitong Gao
Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813 USA
Search for more papers by this authorCorresponding Author
Youping Deng
Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813 USA
E-mail: [email protected]
Search for more papers by this authorTing Gong
Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813 USA
Search for more papers by this authorHeather Borgard
Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813 USA
Search for more papers by this authorZao Zhang
Department of Medicine, The Queen's Medical Center, Honolulu, HI, 96813 USA
Search for more papers by this authorShaoqiu Chen
Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813 USA
Search for more papers by this authorZitong Gao
Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813 USA
Search for more papers by this authorCorresponding Author
Youping Deng
Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813 USA
E-mail: [email protected]
Search for more papers by this authorAbstract
DNA methylation is associated with transcriptional repression, genomic imprinting, stem cell differentiation, embryonic development, and inflammation. Aberrant DNA methylation can indicate disease states, including cancer and neurological disorders. Therefore, the prevalence and location of 5-methylcytosine in the human genome is a topic of interest. Whole-genome bisulfite sequencing (WGBS) is a high-throughput method for analyzing DNA methylation. This technique involves library preparation, alignment, and quality control. Advancements in epigenetic technology have led to an increase in DNA methylation studies. This review compares the detailed experimental methodology of WGBS using accessible and up-to-date analysis tools. Practical codes for WGBS data processing are included as a general guide to assist progress in DNA methylation studies through a comprehensive case study.
Conflict of Interest
The authors declare no conflict of interest.
Open Research
Data Availability Statement
The WGBS raw reads dataset analyzed during the current study are available from the corresponding author upon reasonable request. The Homo sapiens genome assembly GRCh38 (hg38) was obtained from https://hgdownload.soe.ucsc.edu/downloads.html.
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