McPAS-TCR: A manually curated catalogue of pathology-associated T cell receptor sequences

Bioinformatics

Volumn 33, Issue 18, 2017, Pages 2924-2929

  Tickotsky, Nili ^a   Sagiv, Tal ^a   Prilusky, Jaime ^a   Shifrut, Eric ^a   Friedman, Nir ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIGEN; LYMPHOCYTE ANTIGEN RECEPTOR;

ANIMAL; CHEMISTRY; DNA SEQUENCE; GENETIC DATABASE; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; MOUSE; SEQUENCE ANALYSIS;

ANIMALS; ANTIGENS; DATABASES, GENETIC; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICE; RECEPTORS, ANTIGEN, T-CELL; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN;

EID: 85029215405     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btx286     Document Type: Article

References (32)

1. Altman,J.D. et al. (1996) Phenotypic analysis of antigen-specific T lymphocytes. Science, 274, 94-96.
2. Bassing,C.H. et al. (2002) The mechanism and regulation of chromosomal V(D)J recombination. Cell, 109(Suppl), S45-S55.
3. Calis,J.J. and Rosenberg,B.R. (2014) Characterizing immune repertoires by high throughput sequencing: strategies and applications. Trends Immunol., 35, 581-590.
4. Clemente,M.J. et al. (2013) Deep sequencing of the T-cell receptor repertoire in CD8 T-large granular lymphocyte leukemia identifies signature landscapes. Blood, 122, 4077-4085.
5. Cohen,C.J. et al. (2015) Isolation of neoantigen-specific T cells from tumor and peripheral lymphocytes. J. Clin. Invest., 125, 3981-3991.
6. Davis,M.M. and Bjorkman,P.J. (1988) T-cell antigen receptor genes and T-cell recognition. Nature, 334, 395-402.
7. Emerson,R.O. et al. (2017) Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire. Nat Genet., 49, 659-665.
8. Friedensohn,S. et al. (2017) Advanced Methodologies in High-Throughput Sequencing of Immune Repertoires. Trends Biotechnol., 35, 203-214.
9. Gao,F. and Wang,K. (2015) Ligation-anchored PCR unveils immune repertoire of TCR-beta from whole blood. BMC Biotechnol., 15, 39.
10. Heather,J.M. et al. (2017) High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities. Brief Bioinform., DOI: 10.1093/bib/bbw138.
11. Hughes,M.M. et al. (2003) T cell receptor CDR3 loop length repertoire is determined primarily by features of the V(D)J recombination reaction. Eur. J. Immunol., 33, 1568-1575.
12. Hunsucker,S.A. et al. (2015) Peptide/MHC tetramer-based sorting of CD8() T cells to a leukemia antigen yields clonotypes drawn nonspecifically from an underlying restricted repertoire. Cancer Immunol. Res., 3, 228-235.
13. Iwashiro,M. et al. (1993) Multiplicity of virus-encoded helper T-cell epitopes expressed on FBL-3 tumor cells. J. Virol., 67, 4533-4542.
14. Kedzierska,K. et al. (2008) Tracking phenotypically and functionally distinct T cell subsets via T cell repertoire diversity. Mol. Immunol., 45, 607-618.
15. Laydon,D.J. et al. (2015) Estimating T-cell repertoire diversity: limitations of classical estimators and a new approach. Philos. Trans. R Soc. Lond. B Biol. Sci., 370.
16. Lefranc,M.P. et al. (1999) IMGT, the international ImMunoGeneTics database. Nucl. Acids Res., 27, 209-212.
17. Levenshtein,V.I. (1966) Binary codes capable of correcting deletions, insertions and reversals. Soviet Phys. Doklady, 10, 707.
18. Madi,A. et al. (2014) T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity. Genome Res., 24, 1603-1612.
19. Mamedov,I.Z. et al. (2011) Quantitative tracking of T cell clones after haematopoietic stem cell transplantation. EMBOMol. Med., 3, 201-207.
20. Mamedov,I.Z. et al. (2013) Preparing unbiased T-cell receptor and antibody cDNA libraries for the deep next generation sequencing profiling. Front Immunol., 4, 456.
21. Menezes,J.S. et al. (2007) A public T cell clonotype within a heterogeneous autoreactive repertoire is dominant in driving EAE. J. Clin. Invest., 117, 2176-2185.
22. Miconnet,I. et al. (2011) Large TCR diversity of virus-specific CD8 T cells provides the mechanistic basis for massive TCR renewal after antigen exposure. J. Immunol., 186, 7039-7049.
23. Miles,J.J. et al. (2010) Genetic and structural basis for selection of a ubiquitous T cell receptor deployed in Epstein-Barr virus infection. PLoS Pathog., 6, e1001198.
24. Robins,H.S. et al. (2010) Overlap and effective size of the human CD8 T cell receptor repertoire. Sci. Transl. Med., 2, 47ra64.
25. Serana,F. et al. (2009) Identification of a public CDR3 motif and a biased utilization of T-cell receptor V beta and J beta chains in HLA-A2/Melan-A-specific T-cell clonotypes of melanoma patients. J. Transl. Med., 7, 21.
26. Shifrut,E. et al. (2013) T cell-receptor repertoire diversity is compromised in the spleen but not in the bone marrow of aged mice due to private and sporadic clonal expansions. Front. Immunol., CD4, 4-379.
27. Shilyansky,J. et al. (1994) T-cell receptor usage by melanoma-specific clonal and highly oligoclonal tumor-infiltrating lymphocyte lines. Proc. Natl. Acad. Sci. U S A, 91, 2829-2833.
28. Thapa,D.R. et al. (2015) Longitudinal analysis of peripheral blood T cell receptor diversity in patients with systemic lupus erythematosus by nextgeneration sequencing. Arthr. Res. Ther., 17, 132.
29. Turner,S.J. et al. (2006) Structural determinants of T-cell receptor bias in immunity. Nat. Rev. Immunol., 6, 883-894.
30. UniProt, C (2015) UniProt: a hub for protein information. Nucl. Acids Res., 43, D204-D212.
31. Venturi,V. et al. (2008) The molecular basis for public T-cell responses? Nat. Rev. Immunol., 8, 231-238.
32. Vita,R. et al. (2015) The immune epitope database (IEDB) 3.0. Nucl. Acids Res., 43, D405-D412.