The primary goal of VDJdb is to facilitate access to existing information on T-cell receptor antigen specificities, i.e. the ability to recognize certain epitopes in a certain MHC contexts.

The project to create a database containing information on T-cell receptors with known specificity (https://vdjdb.cdr3.net/) was launched in 2015 to aggregate the scarce TCR specificity information available so far and to create a curated repository to store such data.

In addition to routine database updates providing the most up-to-date information fetched from recently published studies utilizing TCR specificity assays, we make our best to ensure data consistency and correct irregularities in TCR specificity reporting with a complex database validation scheme.

Currently, the database functionality has been significantly expanded in terms of the annotating capabilities of “clonsets”, that is, a large number of TKR options obtained using the in-depth NGS analysis.

RELATED PUBLICATIONS

Pogorelyy MV, Minervina AA, Touzel MP, Sycheva AL, Komech EA, Kovalenko EI, Karganova GG, Egorov ES, Komkov AY, Chudakov DM, Mamedov IZ, Mora T, Walczak AM, Lebedev YB. Precise tracking of vaccine-responding T cell clones reveals convergent and personalized response in identical twins. Proc Natl Acad Sci U S A. 2018. 115(50):12704-12709. doi: 10.1073/pnas.1809642115.

Bolotin D.A., Poslavsky S., Davydov A.N., Chudakov D.M. Reply to "Evaluation of immune repertoire inference methods from RNA-seq data". Nature Biotechnology 2018. V. 36. – № 11. – P. 1035-1036. IF 35,724

Shugay M., Bagaev D.V., Zvyagin I.V., Vroomans R.M., Crawford J.C., Dolton G., Komech E.A., Sycheva A.L., Koneva A.E., Egorov E.S., Eliseev A.V., et al. VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. Nucleic Acids Research 2018. № 46. – P. D419-D427. IF 11,561

Bolotin D.A., Poslavsky S., Davydov A.N., Frenkel F.E., Fanchi L., Zolotareva O.I., Hemmers S., Putintseva E.V., Obraztsova A.S., Shugay M., Ataullakhanov R.I., Rudensky A.Y., Schumacher T.N., Chudakov D.M. Antigen receptor repertoire profiling from RNA-seq data. Nature Biotechnology 2017. V. 35. – № 10. – P. 908-911. IF 41,667

Levine A.G., Medoza A., Hemmers S., Moltedo B., Niec R.E., Schizas M., Hoyos B.E., Putintseva E.V., Chaudhry A., Dikiy S., Fujisawa S., Chudakov D.M., Treuting P.M., Rudensky A.Y. Stability and function of regulatory T cells expressing the transcription factor T-bet. Nature 2017. V. 546. – P. 421–425. IF 40,137

Plitas George, Konopacki Catherine, Wu Kenmin, DBos Paula, Morrow Monica, Putintseva Ekaterina, Chudakov Dmitriy M., Rudensky Alexander Y. Regulatory T Cells Exhibit Distinct Features in Human Breast Cancer. Immunity 2016. V. 45. – № 5. – P. 1122-1134. IF 24,082.

Turchaninova M.A., Davydov A., Britanova O.V., Shugay M., Bikos V., Egorov E.S., Kirgizova V.I., Merzlyak E.M., Staroverov D.B., Bolotin D.A., Mamedov I.Z., Izraelson M., Logacheva M.D., Kladova O., Plevova K., Pospisilova S., Chudakov D.M. High-quality full-length immunoglobulin profiling with unique molecular barcoding. Nature Protocols 2016. V. 11. – № 9. – P. 1599–1616. IF 9,646

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Bagaev D.V., Zvyagin I.V., Putintseva E.V., Izraelson M., Britanova O.V., Chudakov D.M., Shugay M. VDJviz: a versatile browser for immunogenomics data. BMC Genomics 2015. V. 17. – № 1. – P. 453. IF 3,867.

Nazarov V.I., Minervina A.A., Komkov A.Y., Pogorelyy M.V., Maschan M.A., Olshanskaya Y.V., Zvyagin I.V., Chudakov D.M., Lebedev Y.B., Mamedov I.Z. Reliability of immune receptor rearrangements as genetic markers for minimal residual disease monitoring. Bone Marrow Transplantation 2015. V. 51. – № 10. – P. 1408-1410. IF 3,636

Feng Y.,van der Veeken J., Shugay M., Putintseva E.V., Osmanbeyoglu H.U., Dikiy S., Hoyos B.E., Moltedo B., Hemmers S., Treuting P., Leslie C. S., Chudakov D.M., Rudensky A.Y. A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance. Nature 2015. V. 528. № 7580. Р. 132-136. IF 41,456.

Bolotin D.A., Poslavsky S., Mitrophanov I., Shugay M., Mamedov I.Z., Putintseva E.V., Chudakov D.M. MiXCR: Software for comprehensive adaptive immunity profiling. Nature Methods 2015. V. 12. № 5. P. 380-381. IF 25,953

Shugay M., Lukyanov S., Chudakov D.M. Sequencing rare T-cell populations. Oncotarget 2015. V. 6. № 37. Р. 39393-39394. IF 6,359

Egorov E.S., Merzlyak E.M., Shelenkov A.A., Britanova O.V., Sharonov G.V., Staroverov D.B., Bolotin D.A., Davydov A.N., Barsova E., Lebedev Y.B., Shugay M., Chudakov D.M. Quantitative profiling of immune repertoires for minor lymphocyte counts using unique molecular identifiers. The Journal of Immunology 2015. V. 194. № 12. Р. 6155-6163. IF 4,922

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