LymAnalyzer: A tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins

Nucleic Acids Research

Volumn 44, Issue 4, 2015, Pages

  Yu, Yaxuan ^a   Ceredig, Rhodri ^a   Seoighe, Cathal ^a  

^a NATIONAL UNIVERSITY OF IRELAND   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN; T LYMPHOCYTE RECEPTOR; LYMPHOCYTE ANTIGEN RECEPTOR;

ALLELE; ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTROLLED STUDY; GENE IDENTIFICATION; GENETIC ALGORITHM; MEASUREMENT ACCURACY; NEXT GENERATION SEQUENCING; PRIORITY JOURNAL; PROTEIN DATABASE; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; VDJ RECOMBINATION; ANIMAL; BIOLOGY; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; MOUSE; PROCEDURES; SOFTWARE;

ANIMALS; COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; IMMUNOGLOBULINS; MICE; RECEPTORS, ANTIGEN, T-CELL; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84960475790     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1016     Document Type: Article

References (22)

1. Wang, C., Sanders, C.M., Yang, Q., Schroeder, H.W., Wang, E., Babrzadeh, F., Gharizadeh, B., Myers, R.M., Hudson, J.R., Davis, R.W. et al. (2010) High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets. Proc. Natl. Acad. Sci. U.S.A., 107, 1518-1523.
2. Clemente, M.J., Przychodzen, B., Jerez, A., Dienes, B.E., Afable, M.G., Husseinzadeh, H., Rajala, H.L., Wlodarski, M.W., Mustjoki, S. and Maciejewski, J.P. (2013) Deep sequencing of the T-cell receptor repertoire in CD8+ T-large granular lymphocyte leukemia identifies signature landscapes. Blood, 122, 4077-4085.
3. Ye, J., Ma, N., Madden, T.L. and Ostell, J.M. (2013) IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res., 41, W34-W40.
4. Brochet, X., Lefranc, M.-P.P. and Giudicelli, V. (2008) IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis. Nucleic Acids Res., 36, W503-W508.
5. Gäeta, B.A., Malming, H.R., Jackson, K.J., Bain, M.E., Wilson, P. and Collins, A.M. (2007) iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences. Bioinformatics, 23, 1580-1587.
6. Thomas, N., Heather, J., Ndifon, W., Shawe-Taylor, J. and Chain, B. (2013) Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine. Bioinformatics, 29, 542-550.
7. Bolotin, D.A., Shugay, M., Mamedov, I.Z., Putintseva, E.V., Turchaninova, M.A., Zvyagin, I.V., Britanova, O.V. and Chudakov, D.M. (2013) MiTCR: software for T-cell receptor sequencing data analysis. Nat. Methods, 10, 813-814.
8. Bolotin, D.A., Poslavsky, S., Mitrophanov, I., Shugay, M., Mamedov, I.Z., Putintseva, E.V. and Chudakov, D.M. (2015) MiXCR: software for comprehensive adaptive immunity profiling. Nat. Methods, 12, 380-381.
9. Lefranc, M.-P.P., Giudicelli, V., Kaas, Q., Duprat, E., Jabado-Michaloud, J., Scaviner, D., Ginestoux, C., Clément, O., Chaume, D. and Lefranc, G. (2005) IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res., 33, D593-D597.
10. Lossos, I.S., Alizadeh, A.A., Eisen, M.B., Chan, W.C., Brown, P.O., Botstein, D., Staudt, L.M. and Levy, R. (2000) Ongoing immunoglobulin somatic mutation in germinal center B cell-like but not in activated B cell-like diffuse large cell lymphomas. Proc. Natl. Acad. Sci. U.S.A., 97, 10209-10213.
11. Putintseva, E., Britanova, O., Staroverov, D., Merzlyak, E., Turchaninova, M., Shugay, M., Bolotin, D., Pogorelyy, M., Mamedov, I., Bobrynina, V. et al. (2013) Mother and child T cell receptor repertoires: deep profiling study. Front. Immunol., 4, 463.
12. Doria-Rose, N., Schramm, C., Gorman, J., Moore, P., Bhiman, J., DeKosky, B., Ernandes, M., Georgiev, I., Kim, H., Pancera, M. et al. (2014) Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies. Nature, 509, 55-62.
13. Boyd, S., Gäeta, B., Jackson, K., Fire, A., Marshall, E., Merker, J., Maniar, J., Zhang, L., Sahaf, B., Jones, C. et al. (2010) Individual variation in the germline ig gene repertoire inferred from variable region gene rearrangements. J. Immunol., 184, 6986-6992.
14. Barak, M., Zuckerman, N., Edelman, H., Unger, R. and Mehr, R. (2008) IgTree©: creating Immunoglobulin variable region gene lineage trees. J. Immunol. Methods, 338, 67-74.
15. Sherry, S.T., Ward, M.-H., Kholodov, M, Baker, J, Phan, L., Smigielski, E.M. and Sirotkin, K. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res., 29, 308-311.
16. Scheepers, C., Shrestha, R.K., Lambson, B.E., Jackson, K.J., Wright, I.A., Naicker, D., Goosen, M., Berrie, L., Ismail, A., Garrett, N. et al. (2015) Ability to develop broadly neutralizing HIV-1 antibodies is not restricted by the germline ig gene repertoire. J. Immunol., 194, 4371-4378.
17. Boyd, S.D., Marshall, E.L., Merker, J.D., Maniar, J.M., Zhang, L.N., Sahaf, B., Jones, C.D., Simen, B.B., Hanczaruk, B., Nguyen, K.D. et al. (2009) Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Sci. Transl. Med., 1, 12ra23.
18. Parameswaran, P., Liu, Y., Roskin, K.M., Jackson, K.K., Dixit, V.P., Lee, J.Y., Artiles, K.L., Zompi, S., Vargas, M.J., Simen, B.B. et al. (2013) Convergent antibody signatures in human dengue. Cell Host Microbe, 13, 691-700.
19. Jackson, K.J., Liu, Y., Roskin, K.M., Glanville, J., Hoh, R.A., Seo, K., Marshall, E.L., Gurley, T.C., Moody, A.M. and Haynes, B.F. (2014) Human responses to influenza vaccination show seroconversion signatures and convergent antibody rearrangements. Cell Host Microbe, 16, 105-114.
20. Wang, C., Liu, Y., Xu, L.T., Jackson, K.J., Roskin, K.M., Pham, T.D., Boyd, S. D et al. (2014) Effects of aging, cytomegalovirus infection, and EBV infection on human B cell repertoires. J. Immunol., 192, 603-611.
21. Wang, Y., Jackson, KJ, Davies, J., Chen, Z., Gaeta, B.A., Rimmer, J., Sewell, W.A. and Collins, A.M. (2014) IgE-associated IGHV genes from venom and peanut allergic individuals lack mutational evidence of antigen selection. PloS One, 9, e89730.
22. Wang, Y., Jackson, K.J., Sewell, W.A. and Collins, A.M. (2008) Many human immunoglobulin heavy-chain IGHV gene polymorphisms have been reported in error. Immunol. Cell Biol., 86, 111-115.