MethPanel

MethPanel analyzes multiplex bisulphite PCR sequencing data to assess DNA methylation biomarker panels for disease detection.

Key Features:

• End-to-end analysis pipeline: Processes data from genomic alignment to DNA methylation calling for multiplex bisulphite PCR sequencing experiments.
• Comprehensive workflow: Supports an unlimited number of PCR amplicons and input samples to accommodate large-scale panels.
• Epipolymorphism score calculation: Computes epipolymorphism scores to assess the impact of genetic polymorphisms on methylation patterns.
• Bisulphite PCR bias correction: Applies corrections for biases introduced during bisulphite conversion and PCR amplification.
• Parallel processing capability: Optimized for parallel execution across multiple samples and high-performance computing environments.
• Centralized data management: Centralizes methylation data storage to facilitate handling of large clinical cohort datasets.

Scientific Applications:

• Methylation biomarker validation: Validates DNA methylation biomarker panels across extensive clinical cohorts for disease detection.
• Sample applicability: Applicable to DNA extracted from fresh tissue, archival formalin-fixed paraffin-embedded tissue (FFPET), and circulating cell-free DNA in plasma.

Methodology:

Performs genomic alignment and DNA methylation calling, computes epipolymorphism scores, applies bisulphite PCR bias correction, and supports parallel execution across samples.