Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Halper Stromberg, Eitan ^a   Steranka, Jared ^b   Giraldo Castillo, Nicolas ^d   Fuller, Timothy ^c,e   Desiderio, Stephen ^b   Burns, Kathleen H ^a,b,c  

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c JOHNS HOPKINS UNIVERSITY   (United States)

^d UNIVERSIDAD DE LOS ANDES   (Colombia)

^e MERCER UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

BCL 2; Lymphoid tumors; MYC; Oncogenic translocation; V replacement; V(D)J recombination

Indexed keywords

GENOMIC DNA; PROTEIN BCL 2; RECOMBINASE;

ARTICLE; B CELL LYMPHOMA; BCL 2 GENE; CANCER CELL; CHROMOSOME TRANSLOCATION; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; LYMPHOBLAST; LYMPHOMA; ONCOGENE MYC; POLYMERASE CHAIN REACTION; VDJ RECOMBINATION; B LYMPHOCYTE; CARCINOGENESIS; CHROMOSOME BREAKAGE; CHROMOSOME MAP; DNA SEQUENCE; ENZYMOLOGY; GENE REARRANGEMENT; GENE TRANSLOCATION; GENETICS; HIGH THROUGHPUT SEQUENCING; LYMPHATIC LEUKEMIA; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; TUMOR CELL LINE;

B-LYMPHOCYTES; BASE SEQUENCE; CARCINOGENESIS; CELL LINE, TUMOR; CHROMOSOME BREAKPOINTS; CHROMOSOME MAPPING; GENE REARRANGEMENT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LEUKEMIA, LYMPHOID; SEQUENCE ANALYSIS, DNA; TRANSLOCATION, GENETIC; VDJ RECOMBINASES;

EID: 84883754153     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-565     Document Type: Article

References (26)

1. Alamyar E, Duroux P, Lefranc MP, Giudicelli V. IMGT((R)) tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS. Methods Mol Biol 2012, 882:569-604. 10.1007/978-1-61779-842-9_32, 22665256.
2. Lefranc MP, Giudicelli V, Busin C, Bodmer J, Muller W, Bontrop R, Lemaitre M, Malik A, Chaume D. IMGT, the International ImMunoGeneTics database. Nucleic Acids Res 1998, 26(1):297-303. 10.1093/nar/26.1.297, 147225, 9399859.
3. Fischer N. Sequencing antibody repertoires: the next generation. mAbs 2011, 3(1):17-20. 10.4161/mabs.3.1.14169, 3038007, 21099370.
4. Watson CT, Breden F. The immunoglobulin heavy chain locus: genetic variation, missing data, and implications for human disease. Genes Immun 2012, 13(5):363-373. 10.1038/gene.2012.12, 22551722.
5. Nilsson K, Klein G. Phenotypic and cytogenetic characteristics of human B-lymphoid cell lines and their relevance for the etiology of Burkitt's lymphoma. Adv Cancer Res 1982, 37:319-380.
6. Wasserman R, Ito Y, Galili N, Yamada M, Reichard BA, Shane S, Lange B, Rovera G. The pattern of joining (JH) gene usage in the human IgH chain is established predominantly at the B precursor cell stage. J Immunol 1992, 149(2):511-516.
7. Huber C, Klobeck HG, Zachau HG. Ongoing V kappa-J kappa recombination after formation of a productive V kappa-J kappa coding joint. Eur J Immunol 1992, 22(6):1561-1565. 10.1002/eji.1830220632, 1601042.
8. Malissen M, McCoy C, Blanc D, Trucy J, Devaux C, Schmitt-Verhulst AM, Fitch F, Hood L, Malissen B. Direct evidence for chromosomal inversion during T-cell receptor beta-gene rearrangements. Nature 1986, 319(6048):28-33. 10.1038/319028a0, 3484541.
9. Fanning L, Bertrand FE, Steinberg C, Wu GE. Molecular mechanisms involved in receptor editing at the Ig heavy chain locus. Int Immunol 1998, 10(2):241-246. 10.1093/intimm/10.2.241, 9533453.
10. Szczepanski T, Pongers-Willemse MJ, Langerak AW, Harts WA, Wijkhuijs AJ, Van Wering ER, Van Dongen JJ. Ig heavy chain gene rearrangements in T-cell acute lymphoblastic leukemia exhibit predominant DH6-19 and DH7-27 gene usage, can result in complete V-D-J rearrangements, and are rare in T-cell receptor alpha beta lineage. Blood 1999, 93(12):4079-4085.
11. Born W, Yague J, Palmer E, Kappler J, Marrack P. Rearrangement of T-cell receptor beta-chain genes during T-cell development. Proc Natl Acad Sci USA 1985, 82(9):2925-2929. 10.1073/pnas.82.9.2925, 397679, 3873070.
12. Kroenlein H, Schwartz S, Reinhardt R, Rieder H, Molkentin M, Gokbuget N, Hoelzer D, Thiel E, Burmeister T. Molecular analysis of the t(2;8)/MYC-IGK translocation in high-grade lymphoma/leukemia by long-distance inverse PCR. Genes Chromosome Canc 2012, 51(3):290-299.
13. Lipford E, Wright JJ, Urba W, Whang-Peng J, Kirsch IR, Raffeld M, Cossman J, Longo DL, Bakhshi A, Korsmeyer SJ. Refinement of lymphoma cytogenetics by the chromosome 18q21 major breakpoint region. Blood 1987, 70(6):1816-1823.
14. Bakhshi A, Wright JJ, Graninger W, Seto M, Owens J, Cossman J, Jensen JP, Goldman P, Korsmeyer SJ. Mechanism of the t(14;18) chromosomal translocation: structural analysis of both derivative 14 and 18 reciprocal partners. Proc Natl Acad Sci U S A 1987, 84(8):2396-2400. 10.1073/pnas.84.8.2396, 304658, 3104914.
15. Kong F, Zhu J, Wu J, Peng J, Wang Y, Wang Q, Fu S, Yuan LL, Li T. dbCRID: a database of chromosomal rearrangements in human diseases. Nucleic Acids Res 2011, 39(Database issue):D895-D900. 3013658, 21051346.
16. Matolcsy A, Casali P, Warnke RA, Knowles DM. Morphologic transformation of follicular lymphoma is associated with somatic mutation of the translocated Bcl-2 gene. Blood 1996, 88(10):3937-3944.
17. Tsai AG, Lu H, Raghavan SC, Muschen M, Hsieh CL, Lieber MR. Human chromosomal translocations at CpG sites and a theoretical basis for their lineage and stage specificity. Cell 2008, 135(6):1130-1142. 10.1016/j.cell.2008.10.035, 2642632, 19070581.
18. Robison K. Application of second-generation sequencing to cancer genomics. Brief Bioinform 2010, 11(5):524-534. 10.1093/bib/bbq013, 20427421.
19. Wiemels JL, Cazzaniga G, Daniotti M, Eden OB, Addison GM, Masera G, Saha V, Biondi A, Greaves MF. Prenatal origin of acute lymphoblastic leukaemia in children. Lancet 1999, 354(9189):1499-1503. 10.1016/S0140-6736(99)09403-9, 10551495.
20. Agrawal A, Eastman QM, Schatz DG. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 1998, 394(6695):744-751. 10.1038/29457, 9723614.
21. Hiom K, Melek M, Gellert M. DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations. Cell 1998, 94(4):463-470. 10.1016/S0092-8674(00)81587-1, 9727489.
22. Giudicelli V, Duroux P, Ginestoux C, Folch G, Jabado-Michaloud J, Chaume D, Lefranc MP. IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences. Nucleic Acids Res 2006, 34(Database issue):D781-D784. 1347451, 16381979.
23. Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res 2002, 12(4):656-664. 187518, 11932250.
24. Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, Mell JC, Hall IM. Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res 2010, 20(5):623-635. 10.1101/gr.102970.109, 2860164, 20308636.
25. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative genomics viewer. Nat Biotechnol 2011, 29(1):24-26. 10.1038/nbt.1754, 3346182, 21221095.
26. Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ. Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 2009, 25(9):1189-1191. 10.1093/bioinformatics/btp033, 2672624, 19151095.