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Diversity of Antigen Receptors

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Antigen receptors are essential components of the immune system crucial in defending the body against foreign invaders. These receptors are present on the surface of B and T cells, enabling them to recognize antigens and mount an appropriate immune response.
Before encountering any antigen, lymphocytes express these receptors. On B cells, the antigen receptor is a membrane-bound antibody molecule called BCR; on T cells, it is a T cell receptor or TCR. B and T cell receptors are composed of two...

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

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Purpose-Built Immunoinformatics for BcR IG/TR Repertoire Data Analysis.

Chrysi Galigalidou^1,2, Laura Zaragoza-Infante^1,3, Anastasia Chatzidimitriou^1,4

¹Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.

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

|May 27, 2022

Summary

Next-generation sequencing reveals complex antigen receptor gene repertoires. The T-cell receptor/immunoglobulin profiler (TRIP) offers a flexible bioinformatics solution for comprehensive immunoprofiling and data analysis.

Keywords:

Antigen receptor B-cell receptor Clonality Immune repertoire Immunoglobulin Immunoinformatics Somatic hypermutation T-cell receptor

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VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

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Published on: December 28, 2015

Area of Science:

Immunology
Bioinformatics
Computational Biology

Background:

Next-generation sequencing (NGS) has uncovered significant complexity in antigen receptor gene repertoires.
Analyzing these complex repertoires necessitates advanced computational and analytical tools.

Purpose of the Study:

To introduce the T-cell receptor/immunoglobulin profiler (TRIP) as a web application for comprehensive antigen receptor repertoire analysis.
To detail TRIP's capabilities in processing IMGT/HighV-Quest output for high-quality immunoprofiling.

Main Methods:

TRIP utilizes R shiny for a user-friendly web application interface.
Data processing involves multi-level filtering of IMGT/HighV-Quest output for quality control.
The workflow includes extraction and analysis of V, D, and J gene segments, CDR3 characterization, and somatic hypermutation analysis.

Main Results:

TRIP enables robust immunoprofiling by analyzing antigen receptor gene rearrangements.
Key analyses include clonality assessment, V(D)J gene repertoire extraction, and detailed CDR3 characterization.
Somatic hypermutation analysis is supported for immunoglobulin rearrangements.

Conclusions:

TRIP provides a flexible and accurate platform for in-depth analysis of antigen receptor gene repertoires.
Customization options in clonotype definition and computation enhance analytical flexibility without sacrificing accuracy.
TRIP addresses the need for novel bioinformatics solutions in repertoire analysis.