VDJviz: a versatile browser for immunogenomics data

Abstract

BackgroundThe repertoire of T- and B-cell receptor sequences encodes the antigen specificity of adaptive immunity system, determines its present state and guides its ability to mount effective response against encountered antigens in future. High throughput sequencing of immune repertoires (Rep-Seq) is a promising technique that allows to profile millions of antigen receptors of an individual in a single experiment. While a substantial number of tools for mapping and assembling Rep-Seq data were published recently, the field still lacks an intuitive and flexible tool that can be used by researchers with little or no computational background for in-depth analysis of immune repertoire profiles.ResultsHere we report VDJviz, a web tool that can be used to browse, analyze and perform quality control of Rep-Seq results generated by various pre-processing software. On a set of real data examples we show that VDJviz can be used to explore key repertoire characteristics such as spectratype, repertoire clonality, V-(D)-J recombination patterns and to identify shared clonotypes. We also demonstrate the utility of VDJviz in detection of critical Rep-Seq biases such as artificial repertoire diversity and cross-sample contamination.ConclusionsVDJviz is a versatile and lightweight tool that can be easily employed by biologists, immunologists and immunogeneticists for routine analysis and quality control of Rep-Seq data. The software is freely available for non-commercial purposes, and can be downloaded from: https://github.com/antigenomics/vdjviz.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2799-7) contains supplementary material, which is available to authorized users.

Graft γδ TCR Sequencing Identifies Public Clonotypes Associated with Hematopoietic Stem Cell Transplantation Efficacy in Acute Myeloid Leukemia Patients and Unravels Cytomegalovirus Impact on Repertoire Distribution

“…Sequencing data were initially analyzed using the ImmunoSEQ Analyzer (https://clients.adaptivebiotech.com/login). Postanalysis of TRG repertoire diversity, clonal space homeostasis, segment usage, spectratyping, and repertoire overlap were performed using the tcR package (35), VDJTools (36), and VDJviz browser (37).…”

Applications of Immunogenomics to Cancer

“…VDJtools (Shugay et al, 2015) is a comprehensive analysis framework for T-cell and B-cell repertoire sequencing data. It includes MIXCR for fast alignment and clonal type assembly (Bolotin et al, 2015), MIGEC for removing duplicates and combining barcodes (Shugay et al, 2014), and VDJviz for visualization (Bagaev et al, 2016), and provides basic statistical analyses for characterizing and comparing different immune repertoires.…”

Systems vaccinology and big data in the vaccine development chain

“…For example, InnateDB contains data on innate immune responses 87 while INTERFEROME focuses on interferon-related processes 88 and the CEMiTool can be used for co-expression analyses and discovery of functionality of genes. 89 For the discovery and analysis of the repertoire of T-and B-cell receptor sequences, VDJviz can be applied for the routine analysis and quality control of sequencing of immune repertoires 90 and VDJdb is designed for the annotation of T-cell receptor repertoire data. 91 These databases evolve and expand continuously based on novel data, scientific insights and technologies.…”