Applications of Next-Generation Sequencing to Blood and Marrow Transplantation

Biology of Blood and Marrow Transplantation

Volumn 18, Issue 1 SUPPL., 2012, Pages

  Chapman, Michael ^a   Warren, Edus H ^b   Wu, Catherine J ^c  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b Fred Hutchinson Cancer Research Center   (United States)

^c DANA FARBER CANCER INSTITUTE   (United States)

Author keywords

Exome sequencing; Genome analysis; TCR; Transplantation

Indexed keywords

B RAF KINASE; DNA; EXPORTIN 1; FLT3 LIGAND; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; ISOCITRATE DEHYDROGENASE; K RAS PROTEIN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2; MESSENGER RNA; MYELOID DIFFERENTIATION FACTOR 88; NOTCH1 RECEPTOR; NUCLEOPHOSMIN; PROTEIN P53; VEMURAFENIB;

ACCURACY; ACUTE GRANULOCYTIC LEUKEMIA; ANTIGEN RECOGNITION; ANTIGEN SPECIFICITY; ARTICLE; B LYMPHOCYTE; CANCER CELL; CANCER GENETICS; CANCER RISK; CD8+ T LYMPHOCYTE; CHRONIC LYMPHATIC LEUKEMIA; CYTOGENETICS; DNA SEQUENCE; EXOME; GENE EXPRESSION; GENE MUTATION; GENE SEQUENCE; GENE TECHNOLOGY; GENOME; GENOME ANALYSIS; GRAFT VERSUS HOST REACTION; GRAFT VERSUS LEUKEMIA EFFECT; HAIRY CELL LEUKEMIA; HEMATOLOGIC MALIGNANCY; HEMATOPOIETIC STEM CELL; HEMATOPOIETIC STEM CELL TRANSPLANTATION; HISTONE METHYLATION; HLA SYSTEM; HUMAN; LYMPHOCYTE; LYMPHOMA; MELANOMA; MEMORY T LYMPHOCYTE; MULTIPLE MYELOMA; MUTATIONAL ANALYSIS; MYELODYSPLASTIC SYNDROME; NEXT GENERATION SEQUENCING; NONHUMAN; ONCOGENE N RAS; PLASMA CELL; PROGNOSIS; RNA SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM; SPLICEOSOME; T LYMPHOCYTE;

ANIMALS; BONE MARROW TRANSPLANTATION; DNA, NEOPLASM; GENE EXPRESSION REGULATION, NEOPLASTIC; GRAFT VS LEUKEMIA EFFECT; HEMATOLOGIC NEOPLASMS; HEMATOPOIETIC STEM CELL TRANSPLANTATION; HUMANS; PROGNOSIS; SEQUENCE ANALYSIS, DNA;

EID: 84855413096     PISSN: 10838791     EISSN: 15236536     Source Type: Journal    
DOI: 10.1016/j.bbmt.2011.11.011     Document Type: Article

References (47)

1. Morozova O., Marra M.A. Applications of next-generation sequencing technologies in functional genomics. Genomics 2008, 92:255-264.
2. Gnirke A., Melnikov A., Maguire J., et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 2009, 27:182-189.
3. Ley T.J., Mardis E.R., Ding L., et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 2008, 456:66-72.
4. Chapman M.A., Lawrence M.S., Keats J.J., et al. Initial genome sequencing and analysis of multiple myeloma. Nature 2011, 471:467-472.
5. Trapnell C., Salzberg S.L. How to map billions of short reads onto genomes. Nat Biotechnol 2009, 27:455-457.
6. Mardis E.R., Ding L., Dooling D.J., et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. NEngl J Med 2009, 361:1058-1066.
7. Paschka P., Schlenk R.F., Gaidzik V.I., et al. IDH1 and IDH2 mutations are frequent genetic alterations in acute myeloid leukemia and confer adverse prognosis in cytogenetically normal acute myeloid leukemia with NPM1 mutation without FLT3 internal tandem duplication. J Clin Oncol 2010, 28:3636-3643.
8. Ley T.J., Ding L., Walter M., et al. DNMT3A mutations in acute myeloid leukemia. N Engl J Med 2010, 363:2424-2433.
9. Annunziata C.M., Davis R.E., Demchenko Y., et al. Frequent engagement of the classical and alternative NF-κB pathways by diverse genetic abnormalities in multiple myeloma. Cancer Cell 2007, 12:115-130.
10. Keats J.J., Fonseca R., Chesi M., et al. Promiscuous mutations activate the non-canonical NF-kB pathway in multiple myeloma. Cancer Cell 2007, 12:131-144.
11. Puente X.S., Pinyol M., Quesada V., et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 2011, 475:101-105.
12. Wang L., Lawrence M.S., Wan Y., et al. SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med 2011, 365.
13. Papaemmanuil E., Cazzola M., Boultwood J., et al. Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts. N Engl J Med 2011, 365:1384-1395.
14. Yoshida K., Sanada M., Shiraishi Y., et al. Frequent pathway mutations of splicing machinery in myelodysplasia. Nature 2011, 478:64-69.
15. Tiacci E., Trifonov V., Schiavoni G., et al. BRAF mutations in hairy-cell leukemia. N Engl J Med 2011, 364:2305-2315.
16. Munroe D.J., Harris T.J.R. Third-generation sequencing fireworks at Marco Island. Nat Biotechnol 2010, 28:426-428.
17. Mardis E.R. A decade's perspective on DNA sequencing technology. Nature 2011, 470:198-203.
18. Boyd S.D., Marshall E.L., Merker J.D., et al. Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Sci Trans Med 2009, 1:1-16.
19. Freeman J.D., Warren R.L., Webb J.R., Nelson B.H., Freeman J.D., Holt R.A. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res 2009, 1817-1824.
20. Robins H.S., Campregher P.V., Srivastava S.K., et al. Comprehensive assessment of T-cell receptor β-chain diversity in αβ T cells. Blood 2009, 114:4099-4107.
21. Wang C., Sanders C.M., 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, 107:1518-1523.
22. Warren R.L., Freeman J.D., 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, 21:790-797.
23. Robins H.S., Srivastava S.K., Campregher P.V., et al. Overlap and effective size of the human CD8+ T cell receptor repertoire. Sci Transl Med 2010, 2:47ra64.
24. Sherwood A.M., Desmarais C., Livingston R.J., et al. Deep sequencing of the human TCRγ and TCRβ repertoires suggests that TCR rearranges after and T cell commitment. Sci Transl Med 2011, 3. 90ra61-90ra61.
25. Kreslavsky T., Gleimer M., Garbe A., vonBoehmer H. αβ versus γδ fate choice: counting the T-cell lineages at the branch point. Immunol Rev 2010, 238:169-181.
26. Kreslavsky T, Boehmer H von. γδ TCR ligands and lineage commitment. Semin Immunol. 2010;22:214-221.
27. Ciofani M., Zúñiga-Pflücker J.C. Determining γδ versus αβ Tcell development. Nat Rev Immunol 2010, 10:657-663.
28. Carding S.R., Egan P.J. γδ T cells: functional plasticity and heterogeneity. Nat Rev Immunol 2002, 2:336-345.
29. Wang H., Fang Z., Morita C.T. Vgamma2Vdelta2 T Cell Receptor recognition of prenyl pyrophosphates is dependent on all CDRs. J Immunol 2010, 184:6209-6222.
30. Kalos M., Levine B.L., Porter D.L., 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. 95ra73.
31. Robins H., Desmarais C., Matthis J., et al. Ultra-sensitive detection of rare T cell clones. J Immunol Methods 2011.
32. Wu C., Ritz J. Induction of tumor immunity following allogeneic stem cell transplantation. Adv Immunol 2006, 90:133-173.
33. Mullally A., Ritz J. Beyond HLA: the significance of genomic variation for allogeneic hematopoietic stem cell transplantation. Blood 2007, 109:1355-1362.
34. Biernacki A.M., Marina O., Zhang W., et al. Efficacious immune therapy in chronic myelogenous leukemia (CML) recognizes antigens that are expressed on CML progenitor cells. Cancer Res 2010, 70:906-915.
35. Zhang W., Choi J., Zeng W., et al. Graft-versus-leukemia antigen CML66 elicits coordinated B-cell and T-cell immunity after donor lymphocyte infusion. Clin Cancer Res 2010, 16:2729-2739.
36. Sensi M., Anichini A. Unique tumor antigens: evidence for immune control of genome integrity and immunogenic targets for T cell-mediated patient-specific immunotherapy. Clin Cancer Res 2006, 12:5023-5032.
37. Parmiani G, Filippo A De, Novellino L, Castelli C. Unique human tumor antigens: immunobiology and use in clinical trials. J Immunol. 2007;178:1975-1979.
38. Mandelboim O., Vadai E., Fridkin M., et al. Regression of established murine carcinoma metastases following vacination with tumour-associated antigen peptides. Nat Med 1995, 1:1179-1183.
39. Zhou J., Shen X., Huang J., Hodes R.J., Rosenberg S.A., Robbins P.F. Telomere length of transferred lymphocytes correlates with invivo persistence and tumor regression in melanoma patients receiving cell transfer therapy. J Immunol 2005, 175:7046-7052.
40. Lennerz V., Fatho M., Gentilini C., et al. The response of autologous T cells to a human melanoma is dominated by mutated neoantigens. Proc Natl Acad Sci USA 2005, 102:16013-16018.
41. Huang J., El-Gamil M., Dudley M.E., Li Y.F., Rosenberg S.A., Robbins P.F. T cells associated with tumor regression recognize frameshifted products of the CDKN2A tumor suppressor gene locus and a mutated HLA class I gene product. J Immunol 2004, 172:6057-6064.
42. Baskar S., Kobrin C.B., Kwak L.W. Autologous lymphoma vaccines induce human T cell responses against multiple, unique epitopes. J Clin Invest 2004, 113:1498-1510.
43. Timmerman J.M., Czerwinski D.K., Davis T.A., et al. Idiotype-pulsed dendritic cell vaccination for B-cell lymphoma: clinical and immune responses in 35 patients. Blood 2002, 99:1517-1526.
44. Sjöblom T., Jones S., Wood L.D., et al. The consensus coding sequences of human breast and colorectal cancers. Science 2006, 314:268-274.
45. Thomas R.K., Baker A.C., Debiasi R.M., et al. High-throughput oncogene mutation profiling in human cancer. Nat Genet 2007, 39:347-351.
46. Segal N.H., Parsons D.W., Peggs K.S., et al. Epitope landscape in breast and colorectal cancer. Cancer Res 2008, 68:889-892.
47. Brusic A, Wu CJ. Anti-cancer vaccines following hematopoietic stem cell transplantation to enhance graft-versus-leukemia responses. Front Biosci (in press).