Novel insights into systemic sclerosis using a sensitive computational method to analyze whole-genome bisulfite sequencing data.

ABSTRACT:

Background

Abnormal DNA methylation is thought to contribute to the onset and progression of systemic sclerosis. Currently, the most comprehensive assay for profiling DNA methylation is whole-genome bisulfite sequencing (WGBS), but its precision depends on read depth and it may be subject to sequencing errors. SOMNiBUS, a method for regional analysis, attempts to overcome some of these limitations. Using SOMNiBUS, we re-analyzed WGBS data previously analyzed using bumphunter, an approach that initially fits single CpG associations, to contrast DNA methylation estimates by both methods.

Methods

Purified CD4+ T lymphocytes of 9 SSc and 4 control females were sequenced using WGBS. We separated the resulting sequencing data into regions with dense CpG data, and differentially me

SUBMITTER: Yu JCY 

PROVIDER: S-EPMC10239181 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature