# CMAtlas: a comprehensive DNA methylation atlas for exploring epigenetic alterations in 34 human cancer types

## TL;DR

CMAtlas is a new platform that maps DNA methylation changes in 34 cancer types, integrating multi-omics data to support precision oncology and drug discovery.

## Contribution

The novel contribution is a comprehensive DNA methylation atlas with deep multi-omics integration across 34 cancer types and 13,753 samples.

## Key findings

- CMAtlas identified 830,725 tumor-specific DMEs and 1,480,098 DMRs across diverse cancer types.
- The platform shows high cross-platform consistency and strong concordance between tumor tissues and cell lines.
- Prognostic methylation patterns in colorectal cancer driver genes were identified using CMAtlas.

## Abstract

Aberrant DNA methylation is a fundamental epigenetic hallmark of cancer. However, existing resources often lack technological diversity and comprehensive cancer coverage. Furthermore, most platforms fail to achieve deep multi-omics integration and tend to ignore cancer-type-specific methylation features, limiting their utility in precision oncology and drug discovery.

We developed Cancer Methylation Atlas (CMAtlas), a comprehensive platform integrating 13 753 samples across 34 cancer types. By applying technology-tailored pipelines to data from various profiling technologies, we identified 830 725 tumor-specific differentially methylated elements (DMEs) and 1 480 098 differentially methylated regions (DMRs), alongside 1 154 256 cancer-type-specific DMEs and 329 154 DMRs. The platform demonstrates high cross-platform consistency and strong concordance between tumor tissues and cell lines, ensuring the robustness of our findings. All DMEs and DMRs are annotated with multi-omics data (RNA expression, somatic mutations, and chromatin accessibility) and clinical relevance (survival associations and cell-free DNA profiling). We further demonstrate the utility of CMAtlas by identifying prognostic aberrant methylation in colorectal cancer driver genes.

CMAtlas is freely accessible at {{https://cmatlas.renlab.cn/}}. The platform offers an intuitive web interface supporting gene-centric and cancer-centric queries, alongside customizable analysis modules designed to facilitate user-specific research needs.