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T and B Cell Receptor Immune Repertoire Analysis using Next-generation Sequencing

T and B Cell Receptor Immune Repertoire Analysis using Next-generation Sequencing

Published on: January 12, 2021

Characterizing immune receptors from new genome sequences.

Katherine M Buckley¹, Jonathan P Rast

¹Department of Immunology and Department of MedicalBiophysics, University of Toronto and Sunnybrook Research Institute, Toronto, Ontario, Canada.

Methods in Molecular Biology (Clifton, N.J.)

|June 25, 2011

Summary

This study presents a computational strategy to identify immune receptors in new genome sequences. The method helps overcome challenges posed by rapid divergence and large gene families, improving immune gene discovery.

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Area of Science:

Genomics
Immunology
Bioinformatics

Background:

Genome sequencing provides vast data on immune mechanisms.
Characterizing immune receptors is challenging due to rapid divergence and large multigene families.
Immune receptors are often overlooked or misannotated in genomic surveys.

Purpose of the Study:

To describe a computational strategy for identifying immune receptor homologs and novel receptors in newly assembled genomes.
To provide protocols accessible to immunologists with limited bioinformatics expertise.
To improve the accuracy of immune gene annotation in large-scale genomic studies.

Main Methods:

Utilizing low-stringency sequence searches to identify divergent immune receptor homologs.
Employing the intersection of low-stringency searches for multi-domain receptors to enhance confidence.
Refining predictions for multigene families using sequence conservation among paralogs.

Main Results:

Successfully identified novel immune receptor expansions in various animal genomes.
Demonstrated the effectiveness of the computational strategy in characterizing immune genes.
The approach is adaptable for identifying immune receptors across diverse species.

Conclusions:

The developed computational strategy accurately identifies immune receptors, including novel ones, in new genome sequences.
This method addresses the specific challenges of immune receptor gene families, improving genomic annotation.
The strategy promises to significantly advance our understanding of animal immunity as more genomes become available.