MethMarker

MethMarker facilitates the design and computational validation of DNA methylation assays for gene-specific differentially methylated regions (DMRs) using assay types such as COBRA, bisulfite SNuPE, bisulfite pyrosequencing, MethyLight, and MSP to support biomarker development in epigenetic studies.

Key Features:

• Assay Design: Designs assays that target differentially methylated regions (DMRs) for COBRA, bisulfite SNuPE, bisulfite pyrosequencing, MethyLight, and MSP.
• Bioinformatic Workflow: Transforms disease-specific DMRs into validated clinical biomarkers through a computational workflow.
• Optimization and Validation: Performs optimization and computational validation of designed assays to evaluate their suitability for large-scale clinical evaluation.
• Clinical Relevance: Enables validation of gene-specific methylation changes across multiple samples to support biomarker use in diagnosis, prognosis, and therapeutic monitoring.

Scientific Applications:

• Cancer epigenetics: Identification and validation of DNA methylation biomarkers for diagnosis, prognosis, and monitoring of therapeutic responses in cancer.
• Biomarker development: Conversion of preidentified DMRs into candidate clinical biomarkers across multiple assay platforms including COBRA, bisulfite SNuPE, bisulfite pyrosequencing, MethyLight, and MSP.

Methodology:

Starting from a preidentified DMR, the methodology applies computational assay design, optimization, and computational validation within a bioinformatic workflow to produce validated clinical biomarkers.