Laboratory research and innovation activities include, among others, development of molecular tools for the basic and biomedical studies, as well development of new methods to identify PCR and sequencing errors and analyze high-throughput sequencing data. Current focus of interest is the role of clonal T cell and B cell populations in autoimmunity and cancer, DNA technologies and software development for the quantitative analysis of individual T cell receptor and antibody repertoires in health and disease.
The main goal is to understand the architecture of human adaptive immunity organisation in health and disease, in development and aging. Tools: high-throughput profiling of T cell receptor and antibody repertoires with the use of unique molecular identifiers (UMI), followed by advanced bioinformatics analysis.
Supervisor – Dmitry Chudakov
|PhD Students:||Sofya Kasatskaya||Varvara Vishniakova||Artem Mikelov|
|Ilya Dyugay||Vadim Karnaukhov|
CD8+ T cells with characteristic T cell receptor beta motif are detected in blood and expanded in synovial fluid of ankylosing spondylitis patients. Komech E, Pogorelyy M, Egorov E, Britanova O, Rebrikov D, Bochkova A, Shmidt E, Shostak N, Shugay M, Lukyanov S, Mamedov I, Lebedev Y, Chudakov D, Zvyagin I. Rheumatology (Oxford). 2018 Feb 22. doi: 10.1093
Comparative analysis of murine T-cell receptor repertoires. Izraelson M, Nakonechnaya T, Moltedo B, Egorov E, Kasatskaya S, Putintseva E, Mamedov I, Staroverov D, Shemiakina I, Zakharova M, Davydov A, Bolotin D, Shugay M, Chudakov D, Rudensky A, Britanova O. Immunology. 2018 Feb;153(2):133-144. doi: 10.1111/imm.12857
VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. Shugay M, Bagaev D, Zvyagin I, Vroomans R, Crawford J, Dolton G, Komech E, Sycheva L, Koneva A, Egorov E, Eliseev A, Van Dyk E, Dash P, Attaf M, Rius C, Ladell K, McLaren J, Matthews K, Clemens E, Douek D, Luciani F, van Baarle D, Kedzierska K, Kesmir C, Thomas P, Price D, Sewell A, Chudakov D. Nucleic Acids Res. 2018 Jan 4;46(D1):D419-D427. doi: 10.1093/nar/gkx760. PMID: 28977646
Antigen receptor repertoire profiling from RNA-seq data. Bolotin D, Poslavsky S, Davydov A, Frenkel F, Fanchi L, Zolotareva O, Hemmers S, Putintseva E, Obraztsova A, Shugay M, Ataullakhanov R, Rudensky A, Schumacher T, Chudakov D. Nat Biotechnol. 2017Oct 11;35(10):908-911. doi: 10.1038/nbt.3979. No abstract available. PMID:29020005
Application of nonsense-mediated primer exclusion (NOPE) for preparation of unique molecular barcoded libraries. Shagin D, Turchaninova M, Shagina I, Shugay M, Zaretsky A, Zueva O, Bolotin D, Lukyanov S, Chudakov D. BMC Genomics. 2017 Jun 5;18(1):440. doi: 10.1186/s12864-017-3815-2.PMID:28583065