Next generation sequencing: New tools in immunology and hematology

Blood Research

Volumn 48, Issue 4, 2013, Pages 242-249

  Mori, Antonio ^a   Deola, Sara ^b   Xumerle, Luciano ^a   Mijatovic, Vladan ^a   Malerba, Giovanni ^a   Monsurrò, Vladia ^a  

^a UNIVERSITY OF VERONA   (Italy)

^b CENTRAL HOSPITAL OF BOLZANO   (Italy)

Author keywords

B cell receptor; Immune monitoring; Next generation sequence; T cell receptor

Indexed keywords

B LYMPHOCYTE RECEPTOR; T LYMPHOCYTE RECEPTOR;

GENETIC PROCEDURES; HELISCOPE SEQUENCING; HEMATOLOGY; HIGH THROUGHPUT SEQUENCING; HUMAN; IMMUNOLOGY; ION TORRENT SEQUENCING; NEOPLASM; NEXT GENERATION SEQUENCING; NONHUMAN; REVIEW;

EID: 84891105152     PISSN: 2287979X     EISSN: 22880011     Source Type: Journal    
DOI: 10.5045/br.2013.48.4.242     Document Type: Review

References (37)

1. Tonegawa S, Steinberg C, Dube S, Bernardini A. Evidence for somatic generation of antibody diversity. Proc Natl Acad Sci U S A 1974;71:4027-31.
2. Tonegawa S. Somatic generation of antibody diversity. Nature 1983;302:575-81.
3. Kim S, Davis M, Sinn E, Patten P, Hood L. Antibody diversity: somatic hypermutation of rearranged VH genes. Cell 1981;27:573-81.
4. Thomas L. On immunosurveillance in human cancer. Yale J Biol Med 1982;55:329-33.
5. Burnet FM. Immunological aspects of malignant disease. Lancet 1967;1:1171-4.
6. Monsurro V, Nagorsen D, Wang E, et al. Functional heterogeneity of vaccine-induced CD8(+) T cells. J Immunol 2002;168:5933-42.
7. Monsurro V, Wang E, Yamano Y, et al. Quiescent phenotype of tumor-specific CD8+ T cells following immunization. Blood 2004;104:1970-8.
8. Pareek CS, Smoczynski R, Tretyn A. Sequencing technologies and genome sequencing. J Appl Genet 2011;52:413-35.
9. Metzker ML. Sequencing technologies-the next generation. Nat Rev Genet 2010;11:31-46.
10. Malone JH, Oliver B. Microarrays, deep sequencing and the true measure of the transcriptome. BMC Biol 2011;9:34.
11. Garber M, Grabherr MG, Guttman M, Trapnell C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods 2011;8:469-77.
12. Bowers J, Mitchell J, Beer E, et al. Virtual terminator nucleotides for next-generation DNA sequencing. Nat Methods 2009;6:593-5.
13. 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;19:1817-24.
14. Robins HS, Campregher PV, Srivastava SK, et al. Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells. Blood 2009;114:4099-107.
15. Robins HS, Srivastava SK, Campregher PV, et al. Overlap and effective size of the human CD8+ T cell receptor repertoire. Sci Transl Med 2010;2:47ra64.
16. Venturi V, Quigley MF, Greenaway HY, et al. A mechanism for TCR sharing between T cell subsets and individuals revealed by pyrosequencing. J Immunol 2011;186:4285-94.
17. 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;21:790-7.
18. Jiang N, Weinstein JA, Penland L, White RA 3rd, Fisher DS, Quake SR. Determinism and stochasticity during maturation of the zebrafish antibody repertoire. Proc Natl Acad Sci U S A 2011;108:5348-53.
19. 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;1:12ra23.
20. Boyd SD, Gaeta BA, Jackson KJ, et al. Individual variation in the germline Ig gene repertoire inferred from variable region gene rearrangements. J Immunol 2010;184:6986-92.
21. Glanville J, Zhai W, Berka J, et al. Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire. Proc Natl Acad Sci U S A 2009;106:20216-21.
22. Ge X, Mazor Y, Hunicke-Smith SP, Ellington AD, Georgiou G. Rapid construction and characterization of synthetic antibody libraries without DNA amplification. Biotechnol Bioeng 2010;106:347-57.
23. Reddy ST, Ge X, Miklos AE, et al. Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells. Nat Biotechnol 2010;28:965-9.
24. Zhai W, Glanville J, Fuhrmann M, et al. Synthetic antibodies designed on natural sequence landscapes. J Mol Biol 2011;412:55-71.
25. Nguyen P, Ma J, Pei D, Obert C, Cheng C, Geiger TL. Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire. BMC Genomics 2011;12:106.
26. Benichou J, Ben-Hamo R, Louzoun Y, Efroni S. Rep-Seq: uncovering the immunological repertoire through next-generation sequencing. Immunology 2012;135:183-91.
27. Rosenwald A, Wright G, Chan WC, et al. The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N Engl J Med 2002;346:1937-47.
28. Dohner K, Dohner H. Molecular characterization of acute myeloid leukemia. Haematologica 2008;93:976-82.
29. Love C, Sun Z, Jima D, et al. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet 2012;44:1321-5.
30. Lenz G, Staudt LM. Aggressive lymphomas. N Engl J Med 2010;362:1417-29.
31. Kohlmann A, Grossmann V, Nadarajah N, Haferlach T. Nextgeneration sequencing-feasibility and practicality in haematology. Br J Haematol 2013;160:736-53.
32. Arber DA, Brunning RD, Le Beau MM, et al. Acute myeloid leukaemia with recurrent genetic abnormalities. In: Swerdlow SH, Campo E, Harris NL, et al, eds. WHO classification of tumours of haematopoietic and lymphoid tissues. 4th ed. Lyon, France: IARC, 2008:110-23.
33. Walter RB, Othus M, Burnett AK, et al. Significance of FAB subclassification of "acute myeloid leukemia, NOS" in the 2008 WHO classification: analysis of 5848 newly diagnosed patients. Blood 2013;121:2424-31.
34. Welch JS, Link DC. Genomics of AML: clinical applications of next-generation sequencing. Hematology Am Soc Hematol Educ Program 2011;2011:30-5.
35. Logan AC, Gao H, Wang C, et al. High-throughput VDJ sequenc ing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment. Proc Natl Acad Sci U S A 2011;108:21194-9.
36. Wu D, Sherwood A, Fromm JR, et al. High-throughput sequencing detects minimal residual disease in acute T lymphoblastic leukemia. Sci Transl Med 2012;4:134ra63.
37. Beck D, Ayers S, Wen J, et al. Integrative analysis of next generation sequencing for small non-coding RNAs and transcriptional regulation in myelodysplastic syndromes. BMC Med Genomics 2011;4:19.