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Identification of Mouse and Human Antibody Repertoires by Next-Generation Sequencing

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An automated algorithm for extracting functional immunologic V-genes from genomes in jawed vertebrates.

David Olivieri¹, Jose Faro, Bernardo von Haeften

¹School of Computer Engineering, University of Vigo, 32004 Ourense, Spain. dnolivieri@gmail.com

|June 25, 2013

Summary

A new bioinformatics tool rapidly identifies functional V-genes, crucial for immunoglobulin (Ig) and T cell receptor (TCR) diversity. This tool aids in comparative genomics and understanding immune system evolution across species.

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Area of Science:

Genomics
Immunology
Bioinformatics

Background:

Variable (V) gene segments are essential for generating immunoglobulin (Ig) and T cell receptor (TCR) diversity.
Current V-gene annotation is limited to a few species, hindering comparative genomic studies.

Purpose of the Study:

To develop and validate a bioinformatics tool for rapid and accurate identification of functional V-genes from genome datasets.
To enable comparative phylogenetic analysis of V-genes across species, including those with incomplete annotations.

Main Methods:

Developed an algorithm recognizing V-gene signatures (recombination signal sequences, exon size, amino acid motifs).
Implemented automated classification of V-genes into TCR or Ig loci.
Validated the tool using human and mouse genomes against public repositories.

Main Results:

The tool accurately identifies functional V-genes, accelerating annotation processes.
Successfully identified V-genes in the rat genome, enabling new comparative analyses.
Comparative analysis supports distinct evolutionary pressures on TCR and Ig V-gene repertoires.

Conclusions:

The developed bioinformatics tool significantly enhances V-gene identification and annotation capabilities.
Facilitates cross-species comparative genomics and evolutionary studies of immune system components.
The open-source software provides a valuable resource for researchers in immunology and genomics.