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Interrogation of clonal tracking data using barcodetrackR.

Diego A Espinoza1,2, Ryland D Mortlock2, Samson J Koelle2,3

  • 1Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

Nature Computational Science
|August 25, 2023
PubMed
Summary
This summary is machine-generated.

This study introduces barcodetrackR, an R package and Shiny app, to standardize the analysis of clonal tracking data. It enables quantitative insights into cellular output for gene and cell therapies, aiding research in lineage reconstitution and vector genotoxicity.

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Area of Science:

  • Biotechnology
  • Bioinformatics
  • Genetics

Background:

  • Clonal tracking methods offer quantitative insights into progenitor cell output over time.
  • These methods are crucial for understanding gene and cell therapies, including lineage reconstitution and vector genotoxicity.
  • A lack of standardized analytical tools has hindered the field of clonal tracking data analysis.

Purpose of the Study:

  • To develop a comprehensive R package and Shiny app, named barcodetrackR, for analyzing and visualizing clonal tracking data.
  • To provide standardized analytical frameworks for the field of clonal tracking.
  • To facilitate the exploration of longitudinal clonal patterns and lineage relationships.

Main Methods:

  • Development of the barcodetrackR R package and accompanying Shiny application.
  • Implementation of diverse tools for quantitative analysis and visualization of clonal tracking data.
  • Application of barcodetrackR to various clonal tracking studies.

Main Results:

  • barcodetrackR provides a toolbox for analyzing clonal tracking data, addressing the previous lack of standardized frameworks.
  • The package and app enable exploration of longitudinal clonal patterns and lineage relationships.
  • Demonstrated utility in studies involving hematopoietic stem and progenitor cells (HSPCs) in human gene therapy and animal models.

Conclusions:

  • barcodetrackR offers a valuable resource for researchers in gene and cell therapy, providing standardized tools for clonal tracking data analysis.
  • The package facilitates deeper understanding of cellular dynamics, lineage reconstitution, and potential genotoxicity.
  • Standardized analysis through barcodetrackR will advance the field of clonal tracking and its applications in therapeutic development.