ChAMP

ChAMP (Chromosome Analysis Methylation Pipeline) is an R package that significantly advances the field of epigenomics by offering a novel solution for identifying differentially methylated regions (DMRs) across the genome. With the advent of the Illumina 450K BeadChip, epigenome-wide association studies (EWAS) have become feasible, producing datasets that can be aligned to genes and genetic features. However, efficiently parsing these datasets to identify discrete DMRs has remained challenging. ChAMP addresses this by introducing the Probe Lasso method, a flexible window-based approach that clusters neighboring significant signals to define DMR boundaries accurately for further analysis.

This method allows for the customization of DMR identification based on user-defined probe filtering criteria and the distribution of probe-lasso sizes, accommodating various research needs. In a practical application using a subset of colon cancer and healthy colon samples from The Cancer Genome Atlas (TCGA), Probe Lasso demonstrated its ability to move beyond merely probe-dense regions, identifying DMRs across a broad range of sizes. Notably, using TCGA data illustrated that Probe Lasso can extract more information from the array than traditional methods. It revealed the potential significance of hypomethylated transcription factor binding motifs, which might not be detected using basic, fixed-window approaches.