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IRProfiler - a software toolbox for high throughput immune receptor profiling.

Christos Maramis1,2, Athanasios Gkoufas3,4, Anna Vardi4

  • 1Lab of Computing, Medical Informatics & Biomedical-Imaging Technologies, Department of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece. chmaramis@med.auth.gr.

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|April 20, 2018
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Summary

Immune repertoire profiling using high-throughput sequencing is crucial for hematological disorders. IRProfiler is a new, user-friendly software tool that efficiently analyzes T-cell and B-cell receptor sequencing data for improved diagnostics.

Keywords:
B-cell receptorsHigh-throughput sequencingImmune receptor profilingSoftware pipelineT-cell receptors

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Area of Science:

  • Bioinformatics
  • Immunology
  • Computational Biology

Background:

  • Immune repertoire profiling is essential for diagnosing and monitoring hematological disorders.
  • High-throughput sequencing (HTS) generates vast amounts of T-cell receptor (TR) and B-cell receptor (BcR) data.
  • Efficient and user-friendly software is needed to analyze this complex immunogenetic data.

Purpose of the Study:

  • Introduce Immune Repertoire Profiler (IRProfiler), a novel software pipeline for analyzing HTS TR and BcR sequencing data.
  • Provide core functionalities for receptor repertoire quantification and comparison.
  • Address the need for efficient and accessible immune repertoire profiling tools.

Main Methods:

  • IRProfiler utilizes 5 alternative clonotype definitions.
  • Includes algorithms for data filtering, clonotype diversity and expression calculation, V/J gene usage analysis, and shared/exclusive clonotype detection.
  • Implemented as a Galaxy bioinformatics platform toolbox with 6 integrated tools.

Main Results:

  • IRProfiler demonstrates scalability with large datasets.
  • Successfully applied in recent studies of hematological disorders.
  • Offers comprehensive analysis of TR and BcR repertoires.

Conclusions:

  • IRProfiler provides added value through support for alternative clonotype definitions and user-centric design.
  • Features include ease-of-use, accessibility, data exploitability, and analysis flexibility.
  • Freely available via multiple distribution channels, including the Galaxy Tool Shed.