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Y-tools: a novel toolkit for analysis of antibody repertoires using immunosequencing data

Name
Yana
Surname
Safonova
Scientific organization
Saint Petersburg State University
Academic degree
Master of Applied Informatics
Position
Junior research fellow
Scientific discipline
Life Sciences & Medicine
Topic
Y-tools: a novel toolkit for analysis of antibody repertoires using immunosequencing data
Abstract
The analysis of circulating antibodies is a fundamental problem in immunoinformatics. Antibodies are not encoded in germline but are diversified by gene recombination and mutations. These processes complicate reconstruction of the original repertoire from sequencing data. On the other hand, antibody repertoire is custom for each individual that results in a lack of gold standard test datasets. To address these challenges, we are developing a toolkit for immunoinformatics analysis including repertoire construction algorithm, tools for clonal and quality assessment analysis.
Keywords
immunoinformatics, personal medicine, immunology, antibody repertoire
Summary

Reconstruction and analysis of antibody repertoire is an important part of various immunological studies. While modern biotechnologies allow one to perform deep and full length scan of circulating antibodies using immunosequencing and mass spectrometry, there is no gold standard toolkit for their analysis. Here we present a novel multipurpose toolkit for construction and investigation of adaptive immune repertoires using immunosequencing and mass spectra data. It includes IgRepertoireConstructor [1], an algorithm for antibody repertoire construction and immunoproteogenomics analysis; AntEvolo, an algorithm for construction of clonal trees and evolutionary analysis of antibody repertoires; aimQUAST [2], a quality assessment tool for adaptive immune repertoires; and IgSimulator [3], a versatile simulator of antibody repertoire. IgRepertoireConstructor, IgSimulator and aimQUAST are freely available at Github. AntEvolo to be released in fall 2016.

[1] Safonova Y, Bonissone S, Kurpilyansky E, Starostina E, Lapidus A, Stinson J, DePalatis L, Sandoval W, Lill J, Pevzner PA. IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis.Bioinformatics. 2015 Jun 15; 31(12): i53-61.

[2] Alexander ShlemovSergey BankevichAndrey BzikadzeYana Safonova. New algorithmic challenges of adaptive immune repertoire construction. Paper accepted at the RECOMB-Seq 2016. doi: arXiv:1604.02193

[3] Safonova Y, Lapidus A, Lill J. IgSimulator: a versatile immunosequencing simulator. Bioinformatics. 2015 Oct 1; 31(19): 3213-5.