VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires
作者： Mikhail Shugay , Dmitriy V Bagaev , Maria A Turchaninova , Dmitriy A Bolotin , Olga V Britanova
DOI: 10.1371/JOURNAL.PCBI.1004503
关键词:
摘要: Despite the growing number of immune repertoire sequencing studies, field still lacks software for analysis and comprehension this high-dimensional data. Here we report VDJtools, a complementary suite that solves wide range T cell receptor (TCR) repertoires post-analysis tasks, provides detailed tabular output publication-ready graphics, is built on top flexible API. Using TCR datasets large cohort unrelated healthy donors, twins, multiple sclerosis patients demonstrate VDJtools greatly facilitates leads to sound biological conclusions. documentation are available at https://github.com/mikessh/vdjtools.
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Eltaf Alamyar, Patrice Duroux, Marie-Paule Lefranc, Véronique Giudicelli, IMGT(®) tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS. Methods of Molecular Biology. ,vol. 882, pp. 569- 604 ,(2012) , 10.1007/978-1-61779-842-9_32
Jorge R. Oksenberg, Michael A. Panzara, Ann B. Begovich, Dennis Mitchell, Henry A. Erlich, Ronald S. Murray, Richard Shimonkevitz, Martina Sherritt, Jonathan Rothbard, Claude C. A. Bernard, Lawrence Steinman, Selection for T-cell receptor Vβ-Dβ-Jβ gene rearrangements with specificity for a myelin basic protein peptide in brain lesions of multiple sclerosis Nature. ,vol. 362, pp. 68- 70 ,(1993) , 10.1038/362068A0
N Flomenberg, B Kissela, C Keever, J Gorski, B Kissella B corrected to Kissela, X Zhu, M Yassai, Circulating T cell repertoire complexity in normal individuals and bone marrow recipients analyzed by CDR3 size spectratyping. Correlation with immune status. Journal of Immunology. ,vol. 152, pp. 5109- 5119 ,(1994)
Kevin Larimore, Michael W. McCormick, Harlan S. Robins, Philip D. Greenberg, Shaping of Human Germline IgH Repertoires Revealed by Deep Sequencing The Journal of Immunology. ,vol. 189, pp. 3221- 3230 ,(2012) , 10.4049/JIMMUNOL.1201303
Claudio Fozza, Magdalena Zoledzieska, Maristella Pitzalis, Maria Pina Simula, Antonio Galleu, Salvatore Contini, Silvana Bonfigli, Francesco Cucca, Maurizio Longinotti, TCRBV20S1 polymorphism does not influence the susceptibility to type 1 diabetes and multiple sclerosis in the Sardinian population Immunogenetics. ,vol. 64, pp. 153- 154 ,(2012) , 10.1007/S00251-011-0575-Z
I. V. Zvyagin, M. V. Pogorelyy, M. E. Ivanova, E. A. Komech, M. Shugay, D. A. Bolotin, A. A. Shelenkov, A. A. Kurnosov, D. B. Staroverov, D. M. Chudakov, Y. B. Lebedev, I. Z. Mamedov, Distinctive properties of identical twins' TCR repertoires revealed by high-throughput sequencing Proceedings of the National Academy of Sciences. ,vol. 111, pp. 5980- 5985 ,(2014) , 10.1073/PNAS.1319389111
Stephen J. Turner, Peter C. Doherty, James McCluskey, Jamie Rossjohn, Structural determinants of T-cell receptor bias in immunity Nature Reviews Immunology. ,vol. 6, pp. 883- 894 ,(2006) , 10.1038/NRI1977
Q. Qi, Y. Liu, Y. Cheng, J. Glanville, D. Zhang, J.-Y. Lee, R. A. Olshen, C. M. Weyand, S. D. Boyd, J. J. Goronzy, Diversity and clonal selection in the human T-cell repertoire. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 111, pp. 13139- 13144 ,(2014) , 10.1073/PNAS.1409155111
Vanessa Venturi, David A. Price, Daniel C. Douek, Miles P. Davenport, The molecular basis for public T-cell responses? Nature Reviews Immunology. ,vol. 8, pp. 231- 238 ,(2008) , 10.1038/NRI2260
M Ladetto, M Brüggemann, L Monitillo, S Ferrero, F Pepin, D Drandi, D Barbero, A Palumbo, R Passera, M Boccadoro, M Ritgen, N Gökbuget, J Zheng, V Carlton, H Trautmann, M Faham, C Pott, Next-generation sequencing and real-time quantitative PCR for minimal residual disease detection in B-cell disorders. Leukemia. ,vol. 28, pp. 1299- 1307 ,(2014) , 10.1038/LEU.2013.375