ImmunExplorer (IMEX): A software framework for diversity and clonality analyses of immunoglobulins and T cell receptors on the basis of IMGT/HighV-QUEST preprocessed NGS data

BMC Bioinformatics

Volumn 16, Issue 1, 2015, Pages

  Schaller, Susanne ^a   Weinberger, Johannes ^b,c   Jimenez Heredia, Raul ^b,c   Danzer, Martin ^b   Oberbauer, Rainer ^d,e   Gabriel, Christian ^b   Winkler, Stephan M ^a  

^a UNIVERSITY OF APPLIED SCIENCES UPPER AUSTRIA   (Austria)

^b Red Cross Blood Transfusion Service of Upper Austria   (Austria)

^c LUDWIG BOLTZMANN INSTITUTE FOR EXPERIMENTAL AND CLINICAL TRAUMATOLOGY   (Austria)

^d ELISABETHINEN HOSPITAL   (Austria)

^e MEDICAL UNIVERSITY OF VIENNA   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODIES; CELL MEMBRANES; CELLS; COMPUTER PROGRAMMING; CYTOLOGY; T-CELLS; VISUALIZATION;

ADAPTIVE IMMUNE SYSTEMS; AMINO ACID SEQUENCE; CALCULATION RESULTS; HUMAN IMMUNE SYSTEMS; IMMUNOLOGICAL REACTIONS; SPLITTING AND MERGING; T-CELL ANTIGEN RECEPTORS; VISUALIZATION EXPERIMENT;

IMMUNE SYSTEM;

DNA; IMMUNOGLOBULIN; LYMPHOCYTE ANTIGEN RECEPTOR; PRIMER DNA;

ALGORITHM; BLOOD; DNA SEQUENCE; GENE REARRANGEMENT; GENETICS; HUMAN; POLYMERASE CHAIN REACTION; SOFTWARE;

ALGORITHMS; DNA; DNA PRIMERS; GENE REARRANGEMENT; HUMANS; IMMUNOGLOBULINS; POLYMERASE CHAIN REACTION; RECEPTORS, ANTIGEN, T-CELL; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84938890197     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-015-0687-9     Document Type: Article

References (22)

1. Lefranc MP, Lefranc G. The immunoglobulin FactsBook. Waltham, Massachusetts: Elsevier; 2001.
2. Lefranc MP. Immunoglobulin and t cell receptor genes: IMGT® and the birth and rise of immunoinformatics. Front Immunol. 2014; 5:22.
3. Abbas AK, Lichtman AHH, Pillai S. Elsevier Health Sci; 1994.
4. Mardis ER. Next-generation sequencing platforms. Annu Rev Anal Chem. 2013; 6(1):287-303.
5. Bolotin DA, Shugay M, Mamedov IZ, Putintseva EV, Turchaninova MA, Zvyagin IV, et al. MiTCR: software for t-cell receptor sequencing data analysis. Nat Methods. 2013; 10(9):813-4.
6. Thomas N, Heather J, Ndifon W, Shawe-Taylor J, Chain B. Decombinator: a tool for fast, efficient gene assignment in t-cell receptor sequences using a finite state machine. Bioinformatics. 2013; 29(5):542-50.
7. Li S, Lefranc MP, Miles JJ, Alamyar E, Giudicelli V, Duroux P, et al. IMGT/HighV QUEST paradigm for t cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling. Nat Commun. 2013; 4:2333.
8. Ye J, Ma N, Madden TL, Ostell JM. IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res. 2013; 41:34-40. doi: http://dx.doi.org/10.1093/nar/gkt382 .
9. Tanneau I, Nondé A, Courtier A, Parmentier G, Noël M, Grivès A, et al. ImmunTraCkeR as a reliable TCR repertoire profiling tool to understand immune response and to explore immunotherapy biomarkers. J Immunother cancer. 2013; 1:112.
10. ImmunoSEQ @ONLINE. http://www.immunoseq.com/ .
11. Rogosch T, Kerzel S, Hoi KH, Zhang Z, Maier RF, Ippolito GC, et al. Front Immunol; 2012.
12. Daelemans W, Van Den Bosch A, Weijters T. IGTree: using trees for compression and classification in lazy learning algorithms. Artif Intell Rev. 1997; 11(1):407-23.
13. Alamyar E, Duroux P, Lefranc MP, Giudicelli V. 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 Mol Biol (Clifton, NJ). 2012; 882:569-604.
14. Brochet X, Lefranc MP, Giudicelli V. 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. 2008; 36:503-8.
15. Yousfi Monod M, Giudicelli V, Chaume D, Lefranc MP. IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and t cell receptor complex v-j and v-d-j JUNCTIONs. Bioinformatics (Oxford, England). 2004; 20 Suppl 1:379-85.
16. Alamyar E, Giudicelli V, Li S, Duroux P, Lefranc MP. IMGT/HighV-QUEST: the IMGT web portal for immunoglobulin (IG) or antibody and t cell receptor (TR) analysis from NGS high throughput and deep sequencing. Immunome res. 2012; 8(1):26.
17. Lefranc MP, Giudicelli V, Duroux P, Jabado-Michaloud J, Folch G, Aouinti S, et al. IMGT®, the international ImMunoGeneTics information system® 25 years on. Nucleic Acids Res. 2015; 43:413-22.
18. Arnaout R, Lee W, Cahill P, Honan T, Sparrow T, Weiand M, et al. High-resolution description of antibody heavy-chain repertoires in humans. PloS One. 2011; 6(8):e22365.
19. Schaller S, Weinberger J, Danzer M, Gabriel C, Oberbauer R, Winkler SM. Mathematical modeling of the diversity in human b- and t-cell receptors using machine learning. Proc 26 th Eur Model Simul Symp. 2014.
20. Rechenberg I. Evolution strategy: nature's way of optimization. In: Optimization: methods and applications, possibilities and limitations. Volume 47. Springer, Lecture Notes in Engineering: 1989. p. 106-26. http://link.springer.com/chapter/10.1007%2F978-3-642-83814-9_6 .
21. van Dongen JJM, Langerak AW, Brüggemann M, Evans PaS, Hummel M, Lavender FL, et al. Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and t-cell receptor gene recombinations in suspect lymphoproliferations: Report of the BIOMED-2 concerted action BMH4-CT98-3936. Leukemia. 2003; 17(12):2257-317.
22. Wagner S, Kronberger G, Beham A, Kommenda M, Scheibenpflug A, Pitzer E, et al. Architecture and Design of the HeuristicLab Optimization Environment. In: Advanced Methods and Applications in Computational Intelligence, Topics in Intelligent Engineering and Informatics Series. Springer: 2014. p. 197-261. http://dev.heuristiclab.com .