VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires

被引：424

作者：

Shugay, Mikhail ^{[1
,2
]}

Bagaev, Dmitriy V. ^{[1
]}

Turchaninova, Maria A. ^{[1
,2
]}

Bolotin, Dmitriy A. ^{[1
,2
]}

Britanova, Olga V. ^{[1
,2
,3
]}

Putintseva, Ekaterina V. ^{[1
,2
,3
]}

Pogorelyy, Mikhail V. ^{[1
]}

Nazarov, Vadim I. ^{[1
,4
]}

Zvyagin, Ivan V. ^{[1
,2
,3
]}

Kirgizova, Vitalina I. ^{[1
]}

Kirgizov, Kirill I. ^{[5
]}

Skorobogatova, Elena V. ^{[5
]}

Chudakov, Dmitriy M. ^{[1
,2
,3
]}

机构：

[1] RAS, Shemyakin Ovchinnikov Inst Bioorgan Chem, Moscow 117901, Russia

[2] Pirogov Russian Natl Res Med Univ, Moscow, Russia

[3] Masaryk Univ, Cent European Inst Technol, Brno, Czech Republic

[4] Natl Res Univ, Higher Sch Econ, Moscow, Russia

[5] Russian Childrens Hosp, Moscow, Russia

来源：

PLOS COMPUTATIONAL BIOLOGY | 2015年 / 11卷 / 11期

基金：

俄罗斯科学基金会;

关键词：

RESIDUAL DISEASE DETECTION; MULTIPLE-SCLEROSIS; CLONAL EXPANSIONS; DEEP; DIVERSITY; GENERATION; SELECTION; SOFTWARE; OVERLAP; EPITOPE;

D O I：

10.1371/journal.pcbi.1004503

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Despite the growing number of immune repertoire sequencing studies, the field still lacks software for analysis and comprehension of this high-dimensional data. Here we report VDJtools, a complementary software suite that solves a wide range of T cell receptor (TCR) repertoires post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API. Using TCR datasets for a large cohort of unrelated healthy donors, twins, and multiple sclerosis patients we demonstrate that VDJtools greatly facilitates the analysis and leads to sound biological conclusions. VDJtools software and documentation are available at https://github.com/mikessh/vdjtools.

引用

页数：16

共 50 条

[41] Sequencing the B Cell Receptor Repertoires of Antibody-Deficient Individuals With and Without Infection Susceptibility
Lim, Yoong Wearn
Ramirez, Neftali Jose
Asensio, Michael A.
Chiang, Yao
Mueller, Gabriele
Mrovecova, Pavla
Mitsuiki, Noriko
Krausz, Mate
Camacho-Ordonez, Nadezhda
Warnatz, Klaus
Adler, Adam S. S.
Grimbacher, Bodo
JOURNAL OF CLINICAL IMMUNOLOGY, 2023, 43 (05) : 940 - 950
[42] Bohemian T cell receptors: sketching the repertoires of unconventional lymphocytes
Schattgen, Stefan A.
Thomas, Paul G.
IMMUNOLOGICAL REVIEWS, 2018, 284 (01) : 79 - 90
[43] tcR: an R package for T cell receptor repertoire advanced data analysis
Nazarov, Vadim I.
Pogorelyy, Mikhail V.
Komech, Ekaterina A.
Zvyagin, Ivan V.
Bolotin, Dmitry A.
Shugay, Mikhail
Chudakov, Dmitry M.
Lebedev, Yury B.
Mamedov, Ilgar Z.
BMC BIOINFORMATICS, 2015, 16
[44] Quantification of Inter-Sample Differences in T-Cell Receptor Repertoires Using Sequence-Based Information
Yokota, Ryo
Kaminaga, Yuki
Kobayashi, Tetsuya J.
FRONTIERS IN IMMUNOLOGY, 2017, 8
[45] The Current Status of T Cell Receptor (TCR) Repertoire Analysis in Colorectal Cancer
Takahashi, Hiroyuki
Hanaoka, Katsuzo
Wada, Hideo
Kojima, Daibo
Watanabe, Masato
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2025, 26 (06)
[46] High frequency of shared clonotypes in human B cell receptor repertoires
Soto, Cinque
Bombardi, Robin G.
Branchizio, Andre
Kose, Nurgun
Matta, Pranathi
Sevy, Alexander M.
Sinkovits, Robert S.
Gilchuk, Pavlo
Finn, Jessica A.
Crowe, James E., Jr.
NATURE, 2019, 566 (7744) : 398 - +
[47] A new high-throughput sequencing method for determining diversity and similarity of T cell receptor (TCR) α and β repertoires and identifying potential new invariant TCR α chains
Kitaura, Kazutaka
Shini, Tadasu
Matsutani, Takaji
Suzuki, Ryuji
BMC IMMUNOLOGY, 2016, 17
[48] Evaluation and comparison of adaptive immunity through analyzing the diversities and clonalities of T-cell receptor repertoires in the peripheral blood
Zhuo, Yue
Yang, Xin
Shuai, Ping
Yang, Liangliang
Wen, Xueping
Zhong, Xuemei
Yang, Shihan
Xu, Shaoxian
Liu, Yuping
Zhang, Zhixin
FRONTIERS IN IMMUNOLOGY, 2022, 13
[49] Genesis of the T-cell receptor
Dupic, Thomas
Marcou, Quentin
Walczak, Aleksandra M.
Mora, Thierry
PLOS COMPUTATIONAL BIOLOGY, 2019, 15 (03)
[50] A Shannon entropy analysis of immunoglobulin and T cell receptor
Stewart, JJ
Lee, CY
Ibrahim, S
Watts, P
Shlomchik, M
Weigert, M
Litwin, S
MOLECULAR IMMUNOLOGY, 1997, 34 (15) : 1067 - 1082

← 1 2 3 4 5 →