mHapBrowser

mHapBrowser analyzes DNA methylation haplotypes (mHaps) derived from bisulfite sequencing to characterize phased methylation patterns across human, mouse, and rat genomes.

Key Features:

• Data processing and integration: Processes bisulfite sequencing datasets from diverse tissues across human, mouse, and rat sourced from public repositories and generates mHap format files for 6,366 samples.
• mHap file generation: Produces standardized mHap format files for all processed samples to support downstream local analyses.
• mHap metrics: Computes eight distinct genome-wide mHap metrics, including the methylation haplotype load (MHL).
• Visualization integration: Integrates with the WashU Epigenome Browser to display the eight mHap metrics across the genome.
• Comparative analysis: Enables comparative analysis of mHap patterns across samples to identify variation and correlations.

Scientific Applications:

• Gene expression correlation: Reveals associations between mHap patterns and gene expression levels.
• Lung cancer subtype analysis: Identifies mHap pattern changes that correlate with differential expression between lung cancer subtypes independent of mean methylation levels.
• Tumor classification from cfDNA: Demonstrates that the MHL metric outperforms mean methylation measures in classifying tumor versus normal samples from cell-free DNA.

Methodology:

Processes bisulfite sequencing data from public repositories for human, mouse, and rat to generate mHap format files for 6,366 samples and compute eight genome-wide mHap metrics for visualization in the WashU Epigenome Browser.