Methylmap: visualization of modified nucleotides for large cohort sizes.

Area of Science:

• Epigenetics and genomics
• Bioinformatics and computational biology

Background:

• Epigenetics, particularly nucleotide modifications like methylation, plays a crucial role in health and disease.
• Understanding methylation patterns at the nucleotide level is essential for advancing epigenetic research.
• Visualizing methylation data, especially for large cohorts, presents a significant challenge.

Purpose of the Study:

• To develop a computational tool for visualizing nucleotide modification frequencies.
• To specifically address the challenge of visualizing methylation data in large cohorts.
• To provide a comprehensive resource for genome-wide methylation pattern analysis.

Main Methods:

• Development of methylmap, a visualization tool for modified nucleotide frequencies.
• Optimization of methylmap for cohort sizes exceeding a few individuals.
• Application of methylmap to visualize haplotype-specific methylation in 226 individuals from the 1000 Genomes Project using Oxford Nanopore Technologies PromethION data.

Main Results:

• Methylmap enables visualization of modified nucleotide frequencies for specific genomic regions.
• The tool successfully visualizes haplotype-specific methylation patterns for a large cohort (226 individuals).
• A comprehensive overview of genome-wide methylation patterns is provided.

Conclusions:

• Methylmap serves as an accessible platform to advance epigenetic research.
• The tool is available as a web application and a command-line tool.
• Methylmap is a valuable resource for understanding epigenetic modifications in health and disease.