High-throughput sequencing of B- And T-lymphocyte antigen receptors in hematology

Blood

Volumn 122, Issue 1, 2013, Pages 19-22

  Warren, Edus H ^a,b   Matsen IV, Frederick A ^a   Chou, Jeffrey ^a,b  

^a Fred Hutchinson Cancer Research Center   (United States)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

B LYMPHOCYTE RECEPTOR; CD4 ANTIGEN; CD8 ANTIGEN; HETERODIMER; T LYMPHOCYTE RECEPTOR; T LYMPHOCYTE RECEPTOR ALPHA CHAIN; T LYMPHOCYTE RECEPTOR BETA CHAIN; T LYMPHOCYTE RECEPTOR GAMMA CHAIN; LYMPHOCYTE ANTIGEN RECEPTOR;

ACUTE LYMPHOBLASTIC LEUKEMIA; ALLOGENEIC HEMATOPOIETIC STEM CELL TRANSPLANTATION; ANTIGEN DETECTION; ARTICLE; B LYMPHOCYTE; CHRONIC LYMPHATIC LEUKEMIA; DNA SEQUENCE; GENE LOCUS; GRAFT RECIPIENT; HEMATOLOGY; HIGH THROUGHPUT SEQUENCING; HUMAN; IMMUNE RECONSTITUTION INFLAMMATORY SYNDROME; LYMPHOCYTE SUBPOPULATION; LYMPHOMA; MEMORY T LYMPHOCYTE; MULTIPLEX POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SPECIES DIVERSITY; T LYMPHOCYTE; CHEMISTRY; DIMERIZATION; EQUIPMENT; GENETICS; HEMATOLOGIC DISEASE; HEMATOPOIETIC STEM CELL TRANSPLANTATION; METHODOLOGY; PATHOLOGY; PROTEIN TERTIARY STRUCTURE; TUMOR EMBOLISM; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; HEMATOLOGIC NEOPLASMS; HEMATOLOGY; HEMATOPOIETIC STEM CELL TRANSPLANTATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; NEOPLASTIC CELLS, CIRCULATING; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, ANTIGEN, B-CELL; RECEPTORS, ANTIGEN, T-CELL, ALPHA-BETA; RECEPTORS, ANTIGEN, T-CELL, GAMMA-DELTA;

EID: 84883721817     PISSN: 00064971     EISSN: 15280020     Source Type: Journal    
DOI: 10.1182/blood-2013-03-453142     Document Type: Article

References (30)

1. Chen JL, Stewart-Jones G, Bossi G, et al. Structural and kinetic basis for heightened immunogenicity of T cell vaccines. J Exp Med. 2005;201(8):1243-1255. (Pubitemid 40629068)
2. Huang J, Ofek G, Laub L, et al. Broad and potent neutralization of HIV-1 by a gp41-specific human antibody. Nature. 2012;491(7424):406-412.
3. The PyMOL Molecular Graphics System, version 1.5.0.5. Schrödinger.
4. Campbell PJ, Pleasance ED, Stephens PJ, et al. Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing. Proc Natl Acad Sci USA. 2008;105(35):13081-13086.
5. Boyd SD, Marshall EL, Merker JD, et al. Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Sci Transl Med. 2009;1(12):12ra23.
6. Wu YC, Kipling D, Leong HS, Martin V, Ademokun AA, Dunn-Walters DK. High-throughput immunoglobulin repertoire analysis distinguishes between human IgM memory and switched memory B-cell populations. Blood. 2010;116(7):1070-1078.
7. Larimore K, McCormick MW, Robins HS, Greenberg PD. Shaping of human germline IgH repertoires revealed by deep sequencing. J Immunol. 2012;189(6):3221-3230.
8. Freeman JD, Warren RL, Webb JR, Nelson BH, Holt RA. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res. 2009;19(10):1817-1824.
9. Robins HS, Campregher PV, Srivastava SK, et al. Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells. Blood. 2009;114(19):4099-4107.
10. Robins HS, Srivastava SK, Campregher PV, et al. Overlap and effective size of the human CD8+ T cell receptor repertoire. Sci Transl Med. 2010;2(47):47ra64.
11. Wang C, Sanders CM, Yang Q, et al. High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets. Proc Natl Acad Sci USA. 2010;107(4):1518-1523.
12. Logan AC, Gao H, Wang C, et al. High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment. Proc Natl Acad Sci USA. 2011;108(52):21194- 21199.
13. Warren RL, Freeman JD, Zeng T, et al. 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 Res. 2011;21(5):790-797.
14. Fisher RA, Corbet AS, Williams CB. The relation between the number of species and the number of individuals in a random sample of an animal population. J Anim Ecol. 1943;12(1):42-58.
15. Efron B, Thisted R. Estimating the number of unseen species: how many words did Shakespeare know? Biometrika. 1976;63(3):435-447.
16. Wang H, Fang Z, Morita CT. Vgamma2Vdelta2 T cell receptor recognition of prenyl pyrophosphates is dependent on all CDRs. J Immunol. 2010;184(11):6209- 6222.
17. Blom B, Verschuren MC, Heemskerk MH, et al. TCR gene rearrangements and expression of the pre-T cell receptor complex during human T-cell differentiation. Blood. 1999;93(9):3033-3043. (Pubitemid 29200796)
18. van Dongen JJ, Langerak AW, Brüggemann M, 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):2257-2317. (Pubitemid 38072572)
19. Sherwood AM, Desmarais C, Livingston RJ, et al. Deep sequencing of the human TCRγ and TCRβ repertoires suggests that TCRβ rearranges after αβ and γδ T cell commitment. Sci Transl Med. 2011;3(90):90ra61.
20. Pacholczyk R, Ignatowicz H, Kraj P, Ignatowicz L. Origin and T cell receptor diversity of Foxp3+ CD4+CD25+ T cells. Immunity. 2006;25(2):249-259. (Pubitemid 44224144)
21. Fazilleau N, Bachelez H, Gougeon ML, Viguier M. Cutting edge: size and diversity of CD4+CD25high Foxp3+ regulatory T cell repertoire in humans: evidence for similarities and partial overlapping with CD4+CD25- T cells. J Immunol. 2007;179(6):3412-3416.
22. Meier J, Roberts C, Avent K, et al. Fractal organization of the human T cell repertoire in health and after stem cell transplantation. Biol Blood Marrow Transplant. 2013;19(3):366-377.
23. van Heijst JW, Ceberio I, Lipuma LB, et al. Quantitative assessment of T cell repertoire recovery after hematopoietic stem cell transplantation. Nat Med. 2013;19(3):372-377.
24. Kalos M, Levine BL, Porter DL, et al. T cells with chimeric antigen receptors have potent antitumor effects and can establish memory in patients with advanced leukemia. Sci Transl Med. 2011;3(95):95ra73.
25. Gawad C, Pepin F, Carlton VE, et al. Massive evolution of the immunoglobulin heavy chain locus in children with B precursor acute lymphoblastic leukemia. Blood. 2012;120(22):4407-4417.
26. Faham M, Zheng J, Moorhead M, et al. Deep-sequencing approach for minimal residual disease detection in acute lymphoblastic leukemia. Blood. 2012;120(26):5173-5180.
27. Brentjens RJ, Davila ML, Riviere I, et al. CD19-targeted T cells rapidly induce molecular remissions in adults with chemotherapy-refractory acute lymphoblastic leukemia. Sci Transl Med. 2013;5(177):177ra38.
28. Wu D, Sherwood A, Fromm JR, et al. High-throughput sequencing detects minimal residual disease in acute T lymphoblastic leukemia. Sci Transl Med. 2012;4(134):134ra63.
29. Kim SM, Bhonsle L, Besgen P, et al. Analysis of the paired TCR α- and β-chains of single human T cells. PLoS ONE. 2012;7(5):e37338.
30. DeKosky BJ, Ippolito GC, Deschner RP, et al. High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire. Nat Biotechnol. 2013;31(2):166-169.