Ig Repertoire Constructor: 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

Research output: Contribution to journalArticlepeer-review

32 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)i53-i61
JournalBioinformatics
Volume31
Issue number12
DOIs
StatePublished - Jun 15 2015

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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