DAMEfinder

DAMEfinder identifies allele-specific DNA methylation and differential ASM regions from bisulfite sequencing data as an R package to study epigenetic regulation such as imprinting and X chromosome inactivation.

Key Features:

• R package implementation: Provided as an R package for analysis of bisulfite sequencing datasets.
• Detection of allele-specific methylation (ASM): Identifies ASM, including genomic imprinting and sequence-dependent ASM (SD-ASM) associated with nearby heterozygous SNPs.
• Differential ASM (DAME) analysis: Detects regions of differential ASM between two conditions.
• ASM scoring system: Calculates an ASM score for all CpG sites or CpG pairs across the genome for each sample.
• Clustering of CpG sites: Clusters nearby CpG sites with consistent changes into regions to define DAMEs.
• Operation without SNP information: Quantifies ASM using sequencing reads alone when SNP data are absent.
• Discrimination of imprinting and XCI: Distinguishes imprinted versus non-imprinted regions and identifies differences related to X chromosome inactivation between females and males.

Scientific Applications:

• Colorectal cancer research: Used to analyze colorectal cancer datasets and distinguish disease subtypes based on ASM signatures.
• Loss of imprinting studies: Re-discovered known cases of loss of imprinting, supporting studies of epigenetic dysregulation in disease.

Methodology:

Uses bisulfite sequencing reads to compute per-sample ASM scores for CpG sites or pairs, clusters nearby CpGs into regions, and performs differential analysis to detect DAMEs between conditions, with the option to quantify ASM without SNP information.