IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis

Yana Safonova; Stefano Bonissone; Eugene Kurpilyansky; Ekaterina Starostina; Alla Lapidus; Jeremy Stinson; Laura DePalatis; Wendy Sandoval; Jennie Lill; Pavel A Pevzner

doi:10.1093/bioinformatics/btv238

IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis

Bioinformatics. 2015 Jun 15;31(12):i53-61. doi: 10.1093/bioinformatics/btv238.

Affiliations

¹ 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 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.
² 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.
³ 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 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 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.

Abstract

The analysis of concentrations of circulating antibodies in serum (antibody repertoire) is a fundamental, yet poorly studied, problem in immunoinformatics. The two current approaches to the analysis of antibody repertoires [next generation sequencing (NGS) and mass spectrometry (MS)] present difficult computational challenges since antibodies are not directly encoded in the germline but are extensively diversified by somatic recombination and hypermutations. Therefore, the protein database required for the interpretation of spectra from circulating antibodies is custom for each individual. Although such a database can be constructed via NGS, the reads generated by NGS are error-prone and even a single nucleotide error precludes identification of a peptide by the standard proteomics tools. Here, we present the IgRepertoireConstructor algorithm that performs error-correction of immunosequencing reads and uses mass spectra to validate the constructed antibody repertoires.

Availability and implementation: IgRepertoireConstructor is open source and freely available as a C++ and Python program running on all Unix-compatible platforms. The source code is available from http://bioinf.spbau.ru/igtools.

Contact: ppevzner@ucsd.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Antibodies / genetics*
Databases, Factual
Genome, Human*
High-Throughput Nucleotide Sequencing / methods*
Humans
Immunoglobulins / analysis*
Mass Spectrometry / methods
Peptide Fragments / analysis
Proteome / analysis*
Sequence Analysis, DNA / methods*
Software*

Substances

Antibodies
Immunoglobulins
Peptide Fragments
Proteome

IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis

Authors

Affiliations

Abstract

Publication types

MeSH terms

Substances

Grants and funding