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

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.eduSupplementary information: Supplementary data are available at Bioinformatics online.

Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads

“…However, transforming an error-prone immunosequencing dataset into an accurate antibody repertoire is a challenging problem that is a prerequisite for a multitude of downstream studies of adaptive immune systems (Figure 1) which include reconstruction of clonal lineages (5, 6), analysis of immune response dynamics (7, 8, 9), analysis of recombination events and secondary diversification (10, 11), immunoproteogenomics (12, 13, 14, 15), and population analysis of Ig germline segments (16). …”

“…Recently, several tools for constructing and annotating full-length antibody repertoires have been developed, including M i GEC (27), p RESTO (28), M i XCR (29), and I g R epertoire C onstructor (14). However, all these tools have limitations making it difficult to benchmark them.…”

Immunoglobulin gene analysis as a tool for investigating human immune responses

“…Methods using paired end Illumina sequencing have advanced, however, allowing the capture of longer reads and sequencing of the full variable region and subclass isotyping with certain 2x 300 bp paired end sequencing methods 74. While Illumina offers unprecedented read counts, reconstructing libraries of antibody sequences, which can be in excess of 900 bp if determining subclass, becomes a bioinformatics conundrum, although there are now a large range of tools to facilitate this 75, 76, 77, 78. Paired end data can also be limited in ability to distinguish some somatic variants 79.…”

Immunoglobulin Classification Using the Colored Antibody Graph

“…The VDJ region of heavy chains is approximately 110 amino acids (330 bp), which is why the previous literature favored the Roche 454 platform due to its larger read lengths of approximately 450 bp. However, with Illumina's increasing read length and throughput, recent and future studies face the challenge of analyzing large repertoires with millions of reads (Safonova et al, 2015).…”

“…This is likely the cause for why so many analyses of Ig-seq experiments produce their own approaches to VDJ classification (Weinstein et al, 2009;Jiang et al, 2011;Arnaout et al, 2011;Wine et al, 2013;Halemano et al, 2014). Even for IgBlast, while scaling well ( Jackson et al, 2010) Roche 454 13 153 3.4 Mouse Ig-seq (Halemano et al, 2014) Illumina MiSeq 204 462 80.0 Human Ig-seq (Safonova et al, 2015) Illumina MiSeq 3 099 967 1 173.0…”