IMMUNE REPERTOIRE AND DISEASE SOFTWARE

To illustrate this, a simple query with “16S rRNA” currently yields more than 8 million records in GenBank, while there are only 37 thousand records annotated as “T-cell receptor”. Moreover, the species phylogeny and annotation is well developed in the field of microbiology, while immune repertoires remain poorly annotated. For example, in technically similar microbiome profiling by 16S rRNA sequencing one deals with thousands of operational taxonomic units that represent various species, while typical TCR repertoire samples may contain hundreds of thousands of clonotypes. Post-analysis of immune repertoire data is a challenging task owing to extreme diversity of TCR and BCR sequences. While such processed data carry nearly exhaustive information on the sampled immune repertoire, this information yet needs to be convolved, scaled and compared across various samples to result in sound biological conclusions. We and others have recently contributed several tools that handle large amounts of raw HTS data to process it into a human-readable list of clonotypes characterized by Variable (V), Diversity (D), Joining (J) segments and V-(D)-J junction sequences of receptor genes.

IMMUNE REPERTOIRE AND DISEASE SOFTWARE

Huge volumes of complex data produced by the immune repertoire profiling have led to the development of a diverse set of software tools, which often complement each other. The advent of high throughput sequencing (HTS) has opened a new venue for the studies of genomics of adaptive immunity that involve deep profiling of T-cell receptor (TCR) and B-cell receptor (BCR) gene repertoires encoding a myriad of antigen specificities. This is a PLOS Computational Biology Software paper The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: The authors have declared that no competing interests exist. The work was carried out in part using equipment provided by the Shemyakin– Ovchinnikov Institute of Bioorganic Chemistry Core Facility.

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedĭata Availability: Raw data for multiple sclerosis patients is deposited at įunding: This work was supported by the Russian Science Foundation project №14-14-00533 (VDJtools development) and RFBR grant 13-04-00998 (cDNA libraries preparation). Received: Accepted: AugPublished: November 25, 2015Ĭopyright: © 2015 Shugay et al. Gardner, University of Canterbury, NEW ZEALAND (2015) VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. The main aims of our framework are: To ensure consistency of post-analysis methods and reproducibility of obtained results to save the time of bioinformaticians analyzing TCR repertoire data by providing comprehensive tabular output and open-source API and to provide a simple enough command line tool so that immunologists and biologists with little computational background could use it to generate publication-ready results.Ĭitation: Shugay M, Bagaev DV, Turchaninova MA, Bolotin DA, Britanova OV, Putintseva EV, et al. Here we present VDJtools, a software framework that can analyze output of most commonly used TCR repertoire processing tools and allows applying a diverse set of post-analysis strategies. Nevertheless, there still exists a major gap in common methods of data post-analysis in the field: there is no standardized data format so far, and most of data comparative analysis is carried out using a variety of in-house scripts. A number of recently developed software tools aim at processing immune repertoire data by mapping Variable (V), Diversity (D) and Joining (J) antigen receptor segments to sequencing reads and assembling T- and B-cell clonotypes. High-throughput profiling of T- and B-cell antigen receptor repertoires promises great advances in our understanding of the mechanisms underlying adaptive immune system function, treatment of autoimmune and infectious diseases, and development of novel approaches in cancer immunotherapy.

Immune repertoire and disease