The database called VDJdb, developed by research group around Dmitriy Chudakov from Masarykova University, helps to reach the next step towards a new level of understanding the adaptive immune system.
Modern sequencing technologies are generating huge numbers of TCR sequences. However, up to now the sequencing data could hardly be linked to functionality of the phenotype TCRs i.e. the ability to recognize certain epitopes presented on a cell surface. Within APERIM finally the comprehensive repository VDJdb was developed, which collects information on TCR sequences with known antigen specificities. The primary goal of this work was to create an open source database and to facilitate access to existing information on T-cell receptor antigen specificities.
Within the cooperation in the APERIM network the establishment of this database is also essential for the development of a further software, called TCR2Epitope. Can Keşmir and her colleagues from the University of Utrecht are working on that visionary tool, which would in the future allow to predict the interaction between TCRs and certain epitopes. The therapeutic application of that tool presents an innovative method to support T cell-mediated cancer immunotherapy.
The infrastructure behind VDJdb allows community-driven data acquisition, proofreading and aggregation in order to establish a comprehensive repository of T-cell receptor sequences with known antigen specifities. The VDJdb database accumulates data from both – previously published papers and obtained via personal communications. Several research groups around the world could be attracted to fulfil the database. Currently the VDJdb includes more than 12000 TCR variants with known specificities and it is rapidly growing.
The database was recently published in Nucleic Acids Research (full paper).
The online database VDJdb is available under https://vdjdb.cdr3.net/