FinaleDB: a browser and database of cell-free DNA fragmentation patterns

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Circulating cell-free DNA (cfDNA) shows potential as a biomarker for diseases like cancer.
• cfDNA fragmentation patterns reflect cellular origins and epigenetic states.
• Limited access to cfDNA whole-genome sequencing (WGS) data hinders computational method development.

Purpose of the Study:

• To establish FinaleDB, a comprehensive database of cfDNA WGS datasets.
• To facilitate the analysis of cfDNA fragmentation patterns.
• To integrate cfDNA data with other omics data for a holistic view.

Main Methods:

• Curated and uniformly processed de-identified cfDNA WGS datasets.
• Development of FinaleDB, a centralized data repository.
• Integration of a fragmentation genome browser with multi-omics data capabilities.

Main Results:

• Thousands of cfDNA WGS datasets are now accessible.
• FinaleDB provides a platform for analyzing genome-wide cfDNA fragmentation.
• Users can visualize cfDNA patterns alongside gene regulation data.

Conclusions:

• FinaleDB addresses the data accessibility bottleneck in cfDNA research.
• The database and browser enhance the study of cfDNA fragmentation mechanisms.
• This resource will accelerate biomarker discovery and disease understanding.