IMonitor: A Robust Pipeline for TCR and BCR Repertoire Analysis

Area of Science:

• Immunology
• Bioinformatics
• Genomics

Background:

• Next-generation sequencing (NGS) enables deep sequencing of T-cell receptors (TCRs) and B-cell receptors (BCRs) to explore immune repertoire diversity.
• Existing analytical tools struggle to efficiently and accurately process the large datasets generated by deep sequencing of immune receptors.

Purpose of the Study:

• To develop a high-resolution analytical pipeline, Immune Monitor (IMonitor), for efficient and accurate processing of immune repertoire sequencing data.
• To compare the performance of IMonitor against existing tools using simulated and public rearranged sequence data.

Main Methods:

• Developed Immune Monitor (IMonitor), a bioinformatics pipeline utilizing realignment for V(D)J gene and allele identification.
• Implemented error correction for PCR and sequencing artifacts, and bias minimization for varying V and J gene families.
• Ensured general adaptation for all receptor chains across different species, with integrated statistics and visualizations.

Main Results:

• IMonitor demonstrated superior performance compared to other published tools in analyzing rearranged sequences.
• The pipeline effectively corrects PCR/sequencing errors and minimizes PCR bias, enhancing data reliability.
• Demonstrated application of IMonitor in minimal residual disease detection for B-cell acute lymphoblastic leukemia patients.

Conclusions:

• IMonitor provides a robust and accurate solution for the analysis of large-scale immune repertoire sequencing data.
• The tool's capabilities in error correction and bias minimization enhance the reliability of immune repertoire studies.
• IMonitor is a valuable package with widespread applicability in immunological research and clinical diagnostics.