Molecular breakpoint analysis of chromosome translocations in cancer cell lines by long distance inverse-PCR

Methods in Molecular Biology

Volumn 731, Issue , 2011, Pages 321-332

  Schneider, Björn ^a   Drexler, Hans G ^a   MacLeod, Roderick A F ^a  

^a NONE

Author keywords

BCL6; Breakpoint; IGH; LDI PCR; MLL; PAX5 translocation

Indexed keywords

COMPLEMENTARY DNA; GENOMIC DNA; MESSENGER RNA;

AMPLICON; ARTICLE; BASE PAIRING; CANCER CELL CULTURE; CELL CLONE; CHROMOSOME ANALYSIS; CHROMOSOME TRANSLOCATION; CYTOGENETICS; DNA PURIFICATION; FLUORESCENCE IN SITU HYBRIDIZATION; GEL ELECTROPHORESIS; GENE AMPLIFICATION; GENE IDENTIFICATION; GENE LOCUS; GENE SEQUENCE; GENOMICS; INVERSE POLYMERASE CHAIN REACTION; LONG DISTANCE INVERSE POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; TUMOR CELL LINE; TUMOR GENE; AGAR GEL ELECTROPHORESIS; CHROMOSOME BREAKAGE; GENE TRANSLOCATION; GENETICS; HUMAN; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION;

BASE SEQUENCE; CELL LINE, TUMOR; CHROMOSOME BREAKPOINTS; ELECTROPHORESIS, AGAR GEL; HUMANS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; TRANSLOCATION, GENETIC;

EID: 84934442564     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-80-5_26     Document Type: Article

References (26)

1. Mitelman, F., Johansson, B., and Mertens, F. (2007) The impact of translocations and gene fusions on cancer causation Nat Rev Cancer 7, 233-45.
2. Turhan, A.G. (2008) BCR (Breakpoint cluster region). Atlas Genet Cytogenet Oncol Haematol. URL: http://AtlasGeneticsOncology.org/Genes/BCR.html.
3. Turhan, A.G. (2008) ABL1 (v-abl Abelson murine leukemia viral oncogene homolog 1). Atlas Genet Cytogenet Oncol Haematol. URL: http:// AtlasGeneticsOncology.org/Genes/ABL.html.
4. Knezevich, S. (2007) BCL6 (B-Cell Lymphoma 6). Atlas Genet Cytogenet Oncol Hematol URL: http://AtlasGeneticsOncology.org/Genes/BCL6ID20.html.
5. Bernard, O.A., Busson-LeConiat, M., Ballerini, P., Mauchauffé, M., Della Valle, V., Monni, R., et al. (2001) A new recurrent and specifc cryptic translocation, t(5;14) (q35;q32), is associated with expression of the Hox11L2 gene in T acute lymphoblastic leukemia Leukemia 15, 1495-504.
6. Nagel, S., Scherr, M., Kel, A., Hornischer, K., Crawford, G.E., Kaufmann, M., et al. (2007) Activation of TLX3 and NKX2-5 in t(5;14) (q35;q32) T-cell acute lymphoblastic leukemia by remote 3¢-BCL11B enhancers and coregula-tion by PU.1 and HMGA1 Cancer Res 67, 1461-71.
7. Meyer, C., Kowarz, E., Hofmann, J., Renneville, A., Zuna, J., Trka, J., et al. (2009) New insights to the MLL recombinome of acute leukemias Leukemia 23, 1490-9.
8. Huret, J.L., and Senon, S. (2003) AML1 (acute myeloid leukemia 1); RUNX1 (runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene)); CBFA2 (core binding factor A2) Atlas Genet Cytogenet Oncol Haematol URL: http://AtlasGeneticsOncology.org/Genes/AML1.html.
9. Kearney, L. (2002) NUP98 (nucleoporin 98 kDa) Atlas Genet Cytogenet Oncol Haematol URL: http://AtlasGeneticsOncology.org/Genes/NUP98.html.
10. Lefranc, M.P. (2003) IGH (Immunoglobulin Heavy) Atlas Genet Cytogenet Oncol Haematol URL: http://AtlasGeneticsOncology.org/Genes/IgHID40.html.
11. MacLeod, R.A.F., Nagel, S., Kaufmann, M., Janssen, J.W.G., and Drexler, H.G. (2003) Activation of HOX11L2 by juxtaposition with 3¢-BCL11B in an acute lymphoblastic leukemia cell line (HPB-ALL) with t(5;14)(q35;q32.2) Genes Chromosomes Cancer 37, 84-91.
12. Schneider, B., Nagel, S., Kaufmann, M., Winkelmann, S., Drexler, H.G., and MacLeod, R.A.F. (2008) T(3;7)(q27;q32) fuses BCL6 to a non-coding region at FRA7H near miR-29 Leukemia 22, 1262-6.
13. Gu, Y., Cimino, G., Alder, H., Nakamura, T., Prasad, R., Canaani, O., et al. (1992) The (4;11)(q21;q23) chromosome translocations in acute leukemias involve the VDJ recombi-nase Proc Natl Acad Sci USA 89, 10464-8.
14. MacLeod, R.A., Dirks, W.G., Matsuo, Y., Kaufmann, M., Milch, H., and Drexler, H.G. (1999) Widespread intraspecies cross-contamination of human tumor cell lines arising at source Int J Cancer 83, 555-63.
15. Frohman, M.A., Dush, M.K., and Martin, G.R. (1988) Rapid production of full-length cDNAs from rare transcripts: amplifcation using a single gene-specifc oligonucleotide primer Proc Natl Acad Sci USA 85, 8998-9002.
16. Ochman, H., Gerber, A.S., and Hartl, D.L. (1988) Genetic applications of an inverse poly-merase chain reaction Genetics 120, 621-3.
17. Willis, T.G., Jadayel, D.M., Coignet, L.J., Abdul-Rauf, M., Treleaven, J.G., Catovsky, D., and Dyer, M.J. (1997) Rapid molecular cloning of rearrangements of the IGHJ locus using long-distance inverse polymerase chain reaction Blood 90, 2456-64.
18. Meyer, C., Schneider, B., Reichel, M., Angermueller, S., Strehl, S., Schnittger, S., et al. (2005) Diagnostic tool for the identif-cation of MLL rearrangements including unknown partner genes Proc Natl Acad Sci USA 102, 449-54.
19. Akasaka, H., Akasaka, T., Kurata, M., Ueda, C., Shimizu, A., Uchiyama, T., and Hitoshi, O. (2000) Molecular anatomy of BCL6 trans-locations revealed by long-distance poly-merase chain reaction-based assays Cancer Res 60, 2335-41.
20. Sonoki, T., Willis, T.G., Oscier, D.G., Karran, E.L., Siebert, R., and Dyer, M.J. (2004) Rapid amplifcation of immunoglobulin heavy chain switch (IGHS) translocation breakpoints using long-distance inverse PCR Leukemia 18, 2026-31.
21. An, Q., Wright, S.L., Konn, Z.J., Matheson, E., Minto, L., Moorman, A.V., et al. (2008) Variable breakpoints target PAX5 in patients with dicentric chromosomes: A model for the basis of unbalanced translocations in cancer Proc Natl Acad Sci USA 105, 17050-4.
22. Megonigal, M.D., Rappaport, E.F., Wilson, R.B., Jones, D.H., Whitlock, J.A., et al. (2000) Panhandle PCR for cDNA: A rapid method for isolation of MLL fusion transcripts involving unknown partner genes Proc Natl Acad Sci USA 97, 9597-602.
23. Tonooka, Y., and Jujishima, F. (2009) Comparison and critical evaluation of PCR-mediated methods to walk along the sequence of genomic DNA Appl Microbiol Biotechnol adv online pub, DOI 10.1007/s00253-009-2211-5.
24. MacLeod, R.A.F., Nagel, S., Scherr, M., Schneider, B., Dirks, W.G., Uphoff, C.C., et al. (2008) Human leukemia and lymphoma cell lines as models and resources Curr Med Chem 15, 339-59.
25. Drexler, H.G. (2001) The Leukemia-Lymphoma Cell Line FactsBook, Academic Press, San Diego.
26. Drexler, H.G. (2009) Guide to Leukemia-Lymphoma Cell Lines, eBook (available from the author), DSMZ, Braunschweig, Germany.