CytoConverter: a web-based tool to convert karyotypes to genomic coordinates

Area of Science:

• Genetics
• Bioinformatics
• Computational Biology

Background:

• Cytogenetic nomenclature describes chromosomal aberrations using bands, while modern genomics uses precise genomic coordinates.
• A gap exists in tools for converting between these two systems.
• This conversion is crucial for identifying genomic features within regions of chromosomal gain or loss.

Purpose of the Study:

• To develop a tool for converting cytogenetic nomenclature to genomic coordinates.
• To facilitate the identification of genomic features affected by chromosomal aberrations.

Main Methods:

• The CytoConverter tool accepts single or multiple karyotypes as input.
• It processes these to identify net chromosomal gains and losses.
• Outputs are provided in standard genomic coordinates.

Main Results:

• CytoConverter successfully converts cytogenetic nomenclature to genomic coordinates.
• It reports net chromosomal gains and losses, including cell counts for aberrations.
• Graphical output visualizing these regions is also generated.

Conclusions:

• CytoConverter bridges the gap between cytogenetic and genomic coordinate systems.
• It is available as a web application and an R script.
• The tool aids in understanding genomic alterations implied by karyotypes.