Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes

Genome Research

Volumn 21, Issue 5, 2011, Pages 790-797

  Warren, René L ^a   Freeman, J Douglas ^a   Zeng, Thomas ^a   Choe, Gina ^a   Munro, Sarah ^a   Moore, Richard ^a   Webb, John R ^a   Holt, Robert A ^a,b  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

^b SIMON FRASER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIGEN; CD45RA ANTIGEN; CD45RO ANTIGEN; HLA ANTIGEN CLASS 1; T LYMPHOCYTE RECEPTOR BETA CHAIN;

ACCURACY; ADULT; AMINO ACID SEQUENCE; ANALYTICAL ERROR; ARTICLE; FEMALE; HUMAN; HUMAN CELL; MALE; MEMORY T LYMPHOCYTE; NORMAL HUMAN; NUCLEOTIDE SEQUENCE; PERIPHERAL BLOOD MONONUCLEAR CELL; PRIORITY JOURNAL; SEQUENCE ANALYSIS; T LYMPHOCYTE;

ADULT; ANTIGENS; FEMALE; GENETIC VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HISTOCOMPATIBILITY ANTIGENS CLASS I; HUMANS; IMMUNOLOGIC MEMORY; LEUKOCYTES, MONONUCLEAR; MALE; RECEPTORS, ANTIGEN, T-CELL, ALPHA-BETA; T-LYMPHOCYTE SUBSETS; T-LYMPHOCYTES;

EID: 79955554975     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.115428.110     Document Type: Article

References (24)

1. Akondy RS, Monson ND, Miller JD, Edupuganti S, Teuwen D, Wu H, Quyyumi F, Garg S, Altman JD, Del Rio C, et al. 2009. The yellow fever virus vaccine induces a broad and polyfunctional human memory CD8+ T cell response. J Immunol 183: 7919-7930.
2. Arstila TP, Casrouge A, Baron V, Even J, Kanellopoulos J, Kourilsky P. 1999. A direct estimate of the human T cell receptor diversity. Science 286: 958-961.
3. Bassing CH, Swat W, Alt FW. 2002. The mechanism and regulation of chromosomal V(D)J recombination. Cell 109(Suppl): S45-S55.
4. Boyd SD, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, Jones CD, Simen BB, Hanczaruk B, Nguyen KD, et al. 2009. Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Sci Transl Med 1: 12ra23.
5. CerebN,Maye P, Lee S, Kong Y, Yang SY. 1995. Locus-specific amplification of HLAclass I genes fromgenomicDNA: Locus-specific sequences in the first and third introns of HLA-A, -B, and -C alleles. Tissue Antigens 45: 1-11.
6. Davis MM, Bjorkman PJ. 1988. T-cell antigen receptor genes and T-cell recognition. Nature 334: 395-402.
7. Deans JP, Boyd AW, Pilarski LM. 1989. Transitions from high to low molecular weight isoforms of CD45 (T200) involve rapid activation of alternate mRNA splicing and slow turnover of surface CD45R. J Immunol 143: 1233-1238. (Pubitemid 19211353)
8. Ewing B, Green P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194.
9. Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, et al. 2010. Ensembl's 10th year. Nucleic Acids Res 38: D557-D562.
10. Freeman JD, Warren RL, Webb JR, Nelson BH, Holt RA. 2009. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res 19: 1817-1824.
11. Harty JT, Badovinac VP. 2008. Shaping and reshaping CD8 T cell memory. Nat Rev Immunol 8: 107-119. (Pubitemid 351161304)
12. Johannisson A, Festin R. 1995. Phenotype transition of CD4+ T cells from CD45RA to CD45R0 is accompanied by cell activation and proliferation. Cytometry 19: 343-352.
13. Khor B, Sleckman BP. 2002. Allelic exclusion at the TCRbeta locus. Curr Opin Immunol 14: 230-234.
14. Klarenbeek PL, Tak PP, van Schaik BD, Zwinderman AH, Jakobs ME, Zhang Z, van Kampen AH, van Lier RA, Baas F, de Vries N. 2010. Human T-cell memory consists mainly of unexpanded clones. Immunol Lett 133: 42-48.
15. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. 2007. Clustal Wand Clustal X version 2.0. Bioinformatics 23: 2947-2948.
16. Marsh SG, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Fernández-Viña M, Geraghty DE, Holdsworth R, Hurley CK, et al. 2010. Nomenclature for factors of the HLA system. 2010. Tissue Antigens 75: 291-455.
17. Nikolich-Zugich J, Slifka MK, Messaoudi I. 2004. The many important facets of T-cell repertoire diversity. Nat Rev Immunol 4: 123-132. (Pubitemid 38209206)
18. Ozawa T, Tajiri K, Kishi H, Muraguchi A. 2008. Comprehensive analysis of the functional TCR repertoire at the single-cell level. Biochem Biophys Res Commun 367: 820-825.
19. Peters DG, Kassam AB, Yonas H, O'Hare EH, Ferrell RE, Brufsky AM. 1999. Comprehensive transcript analysis in small quantities of mRNA by SAGE-lite. Nucleic Acids Res 27: e39. doi: 10.1093/nar/27.24.e39.
20. Robins HS, Campregher PV, Srivastava SK, Wacher A, Turtle CJ, Kahsai O, Riddell SR, Warren EH, Carlson CS. 2009. Comprehensive assessment of T-cell receptor b-chain diversity in ab T cells. Blood 114: 4099-4107.
21. Robins HS, Srivastava SK, Campregher PV, Turtle CJ, Andriesen J, Riddell SR, Carlson CS, Warren EH. 2010. Overlap and effective size of the human CD8+ T cell receptor repertoire. Sci Transl Med 2: 47ra64. doi: 10.1126/scitranslmed. 3001442.
22. Robinson J,Waller MJ, Parham P, de Groot N, Bontrop R, Kennedy LJ, Stoehr P, Marsh SGE. 2003. IMGT/HLA and IMGT/MHC: Sequence databases for the study of the major histocompatibility complex. Nucleic Acids Res 31: 311-314. (Pubitemid 36150392)
23. Slater GS, Birney E. 2005. Automated generation of heuristics for biological sequence comparison.BMC Bioinformatics 6: 31. doi: 10.1186/1471-2105-6-31.
24. Wang C, Sanders CM, Yang Q, Schroeder HW Jr, Wang E, Babrzadeh F, Gharizadeh, Myers B, Hudson RM Jr JR, Davis RW, et al. 2010. High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets. Proc Natl Acad Sci 107: 1518-1523.