TRACE: Open-Source Software for Quantifying Somatic Variation of Tandem Repeats by Capillary Electrophoresis

Area of Science:

• Genetics
• Molecular Biology
• Bioinformatics

Background:

• Expanded short tandem DNA repeats are linked to over 60 human diseases.
• Somatic instability (SI) of these repeats is critical in disease pathogenesis, notably in Huntington's disease.
• Current methods for quantifying SI, like PCR and capillary electrophoresis, often require expensive proprietary software and custom pipelines.

Purpose of the Study:

• To develop an accessible, open-source software for end-to-end analysis of somatic repeat instability.
• To provide a standardized and efficient tool for quantifying SI metrics from fragment analysis data.
• To create an interactive web application for broader user accessibility.

Main Methods:

• Development of Tandem Repeats Analysis by Capillary Electrophoresis (TRACE), an open-source software.
• Creation of TRACE-shiny, an associated web application for interactive use.
• Benchmarking TRACE outputs against published datasets to validate its utility.

Main Results:

• TRACE processes fragment analysis data from raw files to SI metrics.
• The software eliminates the need for proprietary software and custom pipelines.
• Validated utility of TRACE for studying genetic and pharmacological modifiers of SI.

Conclusions:

• TRACE provides a widely accessible, open-source solution for analyzing somatic repeat expansion.
• The developed software and web app streamline the quantification of SI, aiding disease research.
• TRACE facilitates advanced analysis of SI, promoting broader scientific engagement in repeat expansion disorders.