epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data
Journal article, Peer reviewed
Published version

Åpne
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https://hdl.handle.net/11250/3144391Utgivelsesdato
2023Metadata
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- Department of Clinical Science [2492]
- Registrations from Cristin [11244]
Sammendrag
Low-level mosaic epimutations within the BRCA1 gene promoter occur in 5–8% of healthy individuals and are associated with a significantly elevated risk of breast and ovarian cancer. Similar events may also affect other tumor suppressor genes, potentially being a significant contributor to cancer burden. While this opens a new area for translational research, detection of low-level mosaic epigenetic events requires highly sensitive and robust methodology for methylation analysis. We here present epialleleR, a computational framework for sensitive detection, quantification, and visualization of mosaic epimutations in methylation sequencing data. Analyzing simulated and real data sets, we provide in-depth assessments of epialleleR performance and show that linkage to epihaplotype data is necessary to detect low-level methylation events. The epialleleR is freely available at https://github.com/BBCG/epialleleR and https://bioconductor.org/packages/epialleleR/ as an open-source R/Bioconductor package.