epialleleR

epialleleR calls and reports cytosine methylation and frequencies of hypermethylated epialleles at the level of genomic regions or individual cytosines in next-generation sequencing data for sensitive detection, quantification, and visualization of mosaic epimutations.

Key Features:

• Methylation Calling: Calls and reports cytosine methylation using binary alignment map (BAM) files as input.
• Epiallele Frequency Reporting: Reports frequencies of hypermethylated epialleles at the level of genomic regions or individual cytosines.
• Methylation Pattern Extraction: Extracts methylation patterns from sequencing data.
• Methylation Visualization: Visualizes methylation patterns.
• Allele-Specific Methylation Assessment: Assesses allele specificity of methylation through linkage to epihaplotype data.

Scientific Applications:

• Mosaic Epimutation Detection: Enables sensitive detection of low-level mosaic epimutations, such as those occurring in the BRCA1 gene promoter in healthy individuals.
• Cancer Risk Assessment: Supports analysis of epigenetic events in tumor suppressor genes associated with elevated cancer risk.
• Translational Epigenetics Research: Facilitates translational research on mitotically and/or meiotically inherited DNA methylation patterns.

Methodology:

The framework analyzes next-generation sequencing data using BAM files as input and employs linkage to epihaplotype data for detection of low-level methylation events.