RTCR: A pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data

Bioinformatics

Volumn 32, Issue 20, 2016, Pages 3098-3106

  Gerritsen, Bram ^a   Pandit, Aridaman ^a   Andeweg, Arno C ^b   De Boer, Rob J ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

^b ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

LYMPHOCYTE ANTIGEN RECEPTOR;

GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; POLYMERASE CHAIN REACTION; T LYMPHOCYTE;

HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; POLYMERASE CHAIN REACTION; RECEPTORS, ANTIGEN, T-CELL; T-LYMPHOCYTES;

EID: 84995528759     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw339     Document Type: Article

References (39)

1. Alamyar, E., et al. (2012). IMGTVR 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. In: Christiansen, T. Frank Tait, and T. D. Brian Immunogenetics. Humana Press, Springer, Totowa, NJ, pp. 569-604
2. Arstila, T.P., et al. (1999). A direct estimate of the human ab T cell receptor diversity. Science, 286, 958-961
3. Bassing, C.H., et al. (2002). The mechanism and regulation of chromosomal V(D)J recombination. Cell, 109, S45-S55
4. Baum, P.D., et al. (2012). Wrestling with the repertoire: the promise and perils of next generation sequencing for antigen receptors. Eur. J. Immunol., 42, 2834-2839
5. Best, K., et al. (2015). Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding. Scientific reports, 5, 011411, Nature Publishing Group
6. Bolotin, D.A., et al. (2012). Next generation sequencing for TCR repertoire profiling: platform-specific features and correction algorithms: new technology. Eur. J. Immunol., 42, 3073-3083
7. Bolotin, D.A., et al. (2013). MiTCR: software for T-cell receptor sequencing data analysis. Nat. Methods, 10, 813-814
8. Bolotin, D.A., et al. (2015). MiXCR: software for comprehensive adaptive immunity profiling. Nat. Methods, 12, 380-381
9. Calis, J.J., and Rosenberg, B.R. (2014). Characterizing immune repertoires by high throughput sequencing: strategies and applications. Trends Immunol., 35, 581-590
10. Cline, J., et al. (1996). PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Res., 24, 3546-3551
11. Davis, M.M., and Bjorkman, P.J. (1988). T-cell antigen receptor genes and T-cell recognition. Nature, 334, 395-402
12. Egorov, E.S., et al. (2015). Quantitative profiling of immune repertoires for minor lymphocyte counts using unique molecular identifiers. J. Immunol., 194, 6155-6163
13. Freeman, J.D., et al. (2009). Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res., 19, 1817-1824
14. Holt, R.A., and Jones, S.J.M. (2008). The new paradigm of flow cell sequencing. Genome Res., 18, 839-846
15. Huang, W., et al. (2012). ART: a next-generation sequencing read simulator. Bioinformatics, 28, 593-594
16. Kinde, I., et al. (2011). Detection and quantification of rare mutations with massively parallel sequencing. Proc. Natl. Acad. Sci. USA, 108, 9530-9535
17. Kivioja, T., et al. (2012). Counting absolute numbers of molecules using unique molecular identifiers. Nat. Methods, 9, 72-74
18. Klarenbeek, P.L., et al. (2010). Human T-cell memory consists mainly of unexpanded clones. Immunol. Lett., 133, 42-48
19. Kuchenbecker, L., et al. (2015). IMSEQ-A fast and error aware approach to immunogenetic sequence analysis. Bioinformatics, 31, 2963-2971
20. Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359
21. 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
22. Mora, T., et al. (2010). Maximum entropy models for antibody diversity. Proc. Natl. Acad. Sci. USA, 107, 5405-5410
23. Murugan, A., et al. (2012). Statistical inference of the generation probability of T-cell receptors from sequence repertoires. Proc. Natl. Acad. Sci. USA, 109, 16161-16166
24. Ndifon, W., et al. (2012). Chromatin conformation governs T-cell receptor J b gene segment usage. Proc. Natl. Acad. Sci. USA, 109, 15865-15870
25. Nguyen, P., et al. (2011). Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire. BMC Genomics, 12, 106
26. Qi, Q., et al. (2014). Diversity and clonal selection in the human T-cell repertoire. Proc. Natl. Acad. Sci. USA, 111, 13139-13144
27. Robins, H.S., et al. (2009). Comprehensive assessment of T-cell receptor b-chain diversity in ab T cells. Blood, 114, 4099-4107
28. Robins, H.S., et al. (2010). Overlap and effective size of the human CD8+ T cell receptor repertoire. Sci. Transl. Med., 2, 47ra64
29. Shendure, J., and Ji, H. (2008). Next-generation DNA sequencing. Nat. Biotechnol., 26, 1135-1145
30. Shugay, M., et al. (2014). Towards error-free profiling of immune repertoires. Nat. Methods, 11, 653-655
31. Suessmuth, Y., et al. (2015). CMV reactivation drives post-Transplant T cell reconstitution and results in defects in the underlying TCRb repertoire. Blood, 125, 3835-3850
32. Thomas, N., et al. (2013). Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine. Bioinformatics, 29, 542-550
33. Vander Heiden, J.A., et al. (2014). pRESTO: a toolkit for processing highthroughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics, 30, 1930-1932
34. Venturi, V., et al. (2011). A mechanism for TCR sharing between T cell subsets and individuals revealed by pyrosequencing. J. Immunol., 186, 4285-4294
35. Wang, C., et al. (2010). High throughput sequencing reveals a complex pattern of dynamic interrelationships among human t cell subsets. Proc. Natl. Acad. Sci. USA, 107, 1518-1523
36. Warren, R.L., et al. (2009). Profiling model t-cell metagenomes with short reads. Bioinformatics, 25, 458-464
37. Warren, R.L., et al. (2011). Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directlymeasured repertoire size of at least 1 million clonotypes. Genome Res., 21, 790-797
38. Woodsworth, D.J., et al. (2013). Sequence analysis of T-cell repertoires in health and disease. Genome Med, 5, 98
39. Yang, X., et al. (2015). TCRklass: a new K-string-based algorithm for human and mouse TCR repertoire characterization. J. Immunol., 194, 446-454