sciReptor: Analysis of single-cell level immunoglobulin repertoires

BMC Bioinformatics

Volumn 17, Issue 1, 2016, Pages

  Imkeller, Katharina ^a   Arndt, Peter F ^b   Wardemann, Hedda ^a   Busse, Christian E ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

Antigen receptor repertoire; B cell repertoire; Immunoglobulin; Single cell

Indexed keywords

ANTIGENS; CELL MEMBRANES; CYTOLOGY;

ANTIGEN RECEPTORS; B CELLS; BIOINFORMATICS TOOLS; BIOLOGICAL INTERPRETATION; IMMUNOGLOBULIN; IMMUNOGLOBULIN SEQUENCES; NEXT-GENERATION SEQUENCING; SINGLE CELLS;

QUALITY CONTROL;

IMMUNOGLOBULIN; IMMUNOGLOBULIN RECEPTOR;

BIOLOGY; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; IMMUNOGLOBULIN GENE; MOLECULAR GENETICS; PROCEDURES; SINGLE CELL ANALYSIS; SOFTWARE;

COMPUTATIONAL BIOLOGY; GENES, IMMUNOGLOBULIN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; IMMUNOGLOBULINS; MOLECULAR SEQUENCE ANNOTATION; RECEPTORS, IMMUNOLOGIC; SINGLE-CELL ANALYSIS; SOFTWARE;

EID: 84956862861     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-016-0920-1     Document Type: Article

References (16)

1. Andrews SF, Huang Y, Kaur K, Popova LI, Ho IY, Pauli NT, et al.Immune history profoundly affects broadly protective B cell responses to influenza. Sci Transl Med. 2015; 7:316ra192.
2. Huang KY, Rijal P, Schimanski L, Powell TJ, Lin TY, McCauley JW, et al.Focused antibody response to influenza linked to antigenic drift. J Clin Invest. 2015; 125(7):2631-45.
3. Kepler TB, Munshaw S, Wiehe K, Zhang R, Yu JS, Woods CW, et al.Reconstructing a B-cell clonal lineage. II. Mutation, selection, and affinity maturation Front Immunol. 2014; 5:170.
4. Tan YC, Blum LK, Kongpachith S, Ju CH, Cai X, Lindstrom TM, et al.High-throughput sequencing of natively paired antibody chains provides evidence for original antigenic sin shaping the antibody response to influenza vaccination. Clin Immunol. 2014; 151(1):55-65.
5. Busse CE, Czogiel I, Braun P, Arndt PF, Wardemann H.Single-cell based high-throughput sequencing of full-length immunoglobulin heavy and light chain gene. Eur J Immunol. 2014; 44(2):597-603.
6. DeKosky BJ, Ippolito GC, Deschner RP, Lavinder JJ, Wine Y, Rawlings BM, et al.High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire. Nat Biotechnol. 2013; 31(2):166-9.
7. Murugan R, Imkeller K, Busse CE, Wardemann H.Direct high-throughput amplification and sequencing of immunoglobulin genes from single human B cells. Eur J Immunol. 2015; 45(9):2698-700.
8. 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):2.
9. Moorhouse MJ, van Zessen D, IJspeert H, Hiltemann S, Horsman S, van der Spek PJ, et al.ImmunoGlobulin galaxy (IGGalaxy) for simple determination and quantitation of immunoglobulin heavy chain rearrangements from NGS. BMC Immunology. 2015; 15:59.
10. Yu Y, Ceredig R, Seoighe C.LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins. Nucleic Acids Res. 2015. [doi: 10.1093/nar/gkv1016 ].
11. Vander Heiden JA, Yaari G, Uduman M, Stern JNH, O'Connor KC, Hafler DA, et al.pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics. 2014; 30(13):1930-2.
12. Gupta NT, Vander Heiden JA, Uduman M, Gadala-Maria D, Yaari G, Kleinstein SH. Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. Bioinformatics. 2015. [doi: 10.1093/bioinformatics/btv359 ].
13. Weese D, Holtgrewe M, Reinert K.RazerS 3: faster, fully sensitive read mapping. Bioinformatics. 2012; 28(20):2592-9.
14. Ye J, Ma N, Madden TL, Ostell JM. IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res. 2013; 41:W34-W40.
15. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10.
16. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32(5):1792-97.