Scientific Gateway
The iReceptor Plus Scientific Gateway is an excellent tool for detailed understanding of the basic biology underlying diseases of the adaptive immune system and is expected to lead to new vaccines, monoclonal antibodies for cancer and autoimmune treatment, and the many other diseases with a connection to the immune system.
The iReceptor Plus Gateway combines a range of new types of data (Single-Cell, Gene Expression, Clonotype, MHC/Immune Receptor Genotype, and Epitope Specificity data). It also includes the ability to perform advanced analyses on these data without ever leaving the Gateway user interface.
The iReceptor Plus Scientific Gateway’s approach to data integration and analysis will make it easy for researchers to connect personalized immune germline genotypes to naïve and antigen-stimulated immune repertoires (antibody/B-cell and T-cells), all the way through to disease phenotypes.
The iReceptor Plus Science Gateway is built on the recently released v1.4 AIRR Standard from the AIRR Community, enabling researchers to now query single-cell and bulk-sequenced immune repertoire studies based on shared metadata fields, or on new characteristics, such as finding samples with high expression for particular genes.
These searches span over five billion rearrangements across nine repositories in the AIRR Data Commons. The addition of subject level MHC and Immune Receptor genotype to the AIRR Data Commons allow for the searching of this valuable data as well, enabling deeper insight into genetic variability and disease association at the population level.
Single-Cell Immune Profiling
By using the iReceptor Plus Science Gateway software, researchers can easily curate, analyze and share single-cell immune profiling data.
This single-cell approach will enable researchers to link the receptor sequence from each cell (e.g., heavy, and light chain of an antibody, or alpha and beta chain of a T-cell receptor) to the gene expression (e.g., GEX) and detailed binding characteristics of each cell in a sample. This will greatly improve our understanding of why some clones of cells are expanding during a response to a pathogen or during the development of an autoimmune disease, while other clones of cells are being suppressed. Ultimately such new knowledge will result in novel diagnostics and therapeutics, and improved patient care for autoimmune diseases, cancer, and novel pathogens.
iReceptor and Antigen/Epitope Specificity
Recent advances on the iReceptor Science Gateway include the ability to link sequence searches to binding characteristics of the immune receptors, through external databases such as the Immune Epitope Database (IEDB). User searches for CDR3 sequences in the AIRR Data Commons will be supplemented with additional information on antigen/epitope specificity information from IEDB.
iReceptor v4.0 and Integrated Analysis Apps
The iReceptor Plus Scientific Gateway includes integrated analysis capability. Commonly used analysis tools developed by the immunology community have been integrated into the iReceptor Plus Gateway, making it possible to run these tools within the iReceptor Plus user interface without having to download data to the user’s desktop.
Supported analysis tools can be run on any data that is found through the Gateway. Community built analysis tools currently integrated include Immunarch (a B-cell/T-cell repertoire analysis tool) and single-cell tools CellTypist (cell type annotation) and Conga (combined analysis of immune receptors and gene expression).
Additionally, iReceptor Plus has developed two custom Apps to assist users in finding relevant data at the repertoire level: the Statistics App produces summary plots for gene usage and CDR3 length distribution, and the Histogram App performs count statistics on any AIRR field.
iReceptor and running your own Repository
The iReceptor Turnkey Repository is a fully AIRR v1.4 compliant, searchable repository, supporting the loading and querying of rearrangement, clone, single cell/GEX, and genotype data. Fully container based, it is an easy to install platform for curating and managing your data. If you are already running an iReceptor Turnkey repository, the v4.0 release includes repository upgrade scripts that convert your data from an iReceptor v3.0 to an iReceptor v4.0 repository. We encourage research groups that produce AIRR-seq data to consider using the iReceptor Turnkey software as an easy way to curate, manage, and share your data as part of the AIRR Data Commons.