Fragmentstein-facilitating data reuse for cell-free DNA fragment analysis

Area of Science:

• Genomics
• Bioinformatics

Background:

• Limited sharing of sensitive cell-free DNA (cfDNA) genomic data impedes method development.
• Existing data sharing solutions simplify cfDNA data by removing nucleotide information, rendering it incompatible with current bioinformatics software.

Purpose of the Study:

• To develop a bioinformatics tool, Fragmentstein, for converting non-sensitive cfDNA fragmentation data into processable alignment mapping (BAM) files.
• To enable functional analyses of cfDNA data from publicly shared, simplified datasets.

Main Methods:

• Fragmentstein reconstructs BAM files by integrating fragment coordinates with sequence information from a reference genome.
• The tool is implemented in bash and available as open-source software.

Main Results:

• Fragmentstein successfully converts non-sensitive cfDNA fragmentation data into BAM files.
• Demonstrated feasibility of copy number variant (CNV), nucleosome occupancy, and fragment length analyses using reconstructed data.

Conclusions:

• Fragmentstein facilitates cfDNA data sharing and analysis by enabling the use of simplified, non-sensitive fragmentation data.
• The tool supports key genomic analyses, overcoming limitations of current bioinformatics software and promoting wider data accessibility.