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Updated: Apr 10, 2026
Identification of Mouse and Human Antibody Repertoires by Next-Generation Sequencing
Published on: March 15, 2019
IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis
Yana Safonova1, Stefano Bonissone2, Eugene Kurpilyansky2
1Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA.
We developed IgRepertoireConstructor to correct errors in immunosequencing reads. This algorithm validates antibody repertoires using mass spectrometry, improving immunoinformatics analysis.
Area of Science:
- Immunoinformatics
- Computational Biology
- Proteomics
Background:
- Analyzing circulating antibody concentrations (antibody repertoire) is crucial but underexplored in immunoinformatics.
- Current methods like next-generation sequencing (NGS) and mass spectrometry (MS) face computational hurdles due to antibody diversification.
- Standard proteomics tools struggle with error-prone NGS reads, hindering peptide identification.
Purpose of the Study:
- To present the IgRepertoireConstructor algorithm for error-correction of immunosequencing reads.
- To enable validation of constructed antibody repertoires using mass spectra.
- To address computational challenges in antibody repertoire analysis.
Main Methods:
- Developed the IgRepertoireConstructor algorithm for immunosequencing read error-correction.
- Utilized mass spectrometry data to validate the accuracy of constructed antibody repertoires.
- Implemented the algorithm in C++ and Python for broad accessibility.
Main Results:
- IgRepertoireConstructor successfully performs error-correction on immunosequencing reads.
- The algorithm enables validation of antibody repertoires, overcoming limitations of standard proteomics tools.
- Provides a computational solution for analyzing complex antibody repertoires.
Conclusions:
- IgRepertoireConstructor offers a robust method for analyzing antibody repertoires.
- The algorithm improves the accuracy and reliability of immunoinformatics studies.
- Facilitates deeper understanding of antibody diversity and function.
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