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 GongHeather BorgardZao ZhangShaoqiu ChenZitong GaoYouping DengPublished in: Small methods (2022)
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.
Keyphrases
- dna methylation
- genome wide
- gene expression
- high throughput
- copy number
- quality control
- electronic health record
- endothelial cells
- oxidative stress
- squamous cell carcinoma
- big data
- case control
- data analysis
- papillary thyroid
- high resolution
- mass spectrometry
- tandem mass spectrometry
- artificial intelligence
- liquid chromatography