MassArray

MassArray processes and analyzes bisulfite-converted DNA methylation data from Sequenom EpiTYPER MALDI-TOF output to enable quantitative assessment of DNA cytosine methylation for epigenetic profiling.

Key Features:

• Assay Design and Optimization: Provides amplicon prediction capabilities to support optimal assay design.
• Quality Control Measures: Estimates bisulfite conversion efficiency and detects primer dimers for data quality assessment.
• Data Analysis Pipeline: Consumes standard Sequenom output files to calculate bisulfite conversion efficiency, flag sequence polymorphisms, and integrate multiple experimental replicates.
• Visualization Tools: Generates genome browser tracks and combines results from multiple experiments for interpretation of methylation patterns.
• Sequenom EpiTYPER / MALDI-TOF Support: Processes and integrates data produced by the Sequenom MassArray EpiTYPER MALDI-TOF assay from bisulfite-treated DNA.
• R Package Implementation: Implements analysis and visualization functionality within an R package.

Scientific Applications:

• Epigenetic Regulation Studies: Supports investigations of DNA cytosine methylation roles in gene regulation, mammalian development, and disease.
• Assay Validation and Quantitative Profiling: Enables quantitative validation of genome-wide cytosine methylation assays using MALDI-TOF EpiTYPER data and facilitates precise epigenetic profiling.

Methodology:

Uses Sequenom MassArray (EpiTYPER) MALDI-TOF output as input; calculates bisulfite conversion efficiency; detects primer dimers; flags sequence polymorphisms; integrates experimental replicates; generates genome browser tracks; implemented as an R package.