Abstract
Recent technological advances in immune repertoire sequencing have created tremendous potential for advancing our understanding of adaptive immune response dynamics in various states of health and disease. Immune repertoire sequencing produces large, highly complex data sets, however, which require specialized methods and software tools for their effective analysis and interpretation. VDJServer is a cloud-based analysis portal for immune repertoire sequence data that provide access to a suite of tools for a complete analysis workflow, including modules for preprocessing and quality control of sequence reads, V(D)J gene segment assignment, repertoire characterization, and repertoire comparison. VDJServer also provides sophisticated visualizations for exploratory analysis. It is accessible through a standard web browser via a graphical user interface designed for use by immunologists, clinicians, and bioinformatics researchers. VDJServer provides a data commons for public sharing of repertoire sequencing data, as well as private sharing of data between users. We describe the main functionality and architecture of VDJServer and demonstrate its capabilities with use cases from cancer immunology and autoimmunity. VDJServer provides a complete analysis suite for human and mouse T-cell and B-cell receptor repertoire sequencing data. The combination of its user-friendly interface and high-performance computing allows large immune repertoire sequencing projects to be analyzed with no programming or software installation required. VDJServer is a web-accessible cloud platform that provides access through a graphical user interface to a data management infrastructure, a collection of analysis tools covering all steps in an analysis, and an infrastructure for sharing data along with workflows, results, and computational provenance. VDJServer is a free, publicly available, and open-source licensed resource.
Highlights
Recent technological advances in immune repertoire sequencing have created tremendous potential for advancing our understanding of adaptive immune response dynamics in various states of health and disease
As part of that effort, we developed VDJServer to address critical barriers in broader adoption of immune repertoire sequencing, namely, the lack of a complete, start-to-finish analysis pipeline, the lack of a data management infrastructure, and limited access for many researchers to high-performance computing (HPC) resources
B cells were obtained from the cerebrospinal fluid (CSF) of patients diagnosed with either relapsing–remitting multiple sclerosis (RRMS) or other neurological disease (OND)
Summary
Recent technological advances in immune repertoire sequencing have created tremendous potential for advancing our understanding of adaptive immune response dynamics in various states of health and disease. The adaptive immune system is composed of specialized cells, molecules, and processes that evolved to defend the organism against foreign pathogens and tumorous cells. The full collection of functional immune receptor gene sequences in an individual at a single point in time is referred to as the adap tive immune receptor repertoire (AIRR). Somatic generation of a tremendously diverse repertoire enables effective immune res ponses against an essentially infinite array of antigens, such as those derived from pathogens or tumors. Components of this somatically generated repertoire can recognize self-antigens, leading to autoimmune responses
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