Reconstructing tumor amplisomes

Bioinformatics

Volumn 20, Issue SUPPL. 1, 2004, Pages

  Raphael, Benjamin J ^a   Pevzner, Pavel A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BREAST CANCER; CANCER CELL CULTURE; CHROMOSOME; CONFERENCE PAPER; DNA SEQUENCE; GENE MAPPING; HUMAN; PRIORITY JOURNAL; TUMOR CELL;

EID: 24044529257     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth931     Document Type: Conference Paper

References (20)

1. Albertson, D., Collins, C., McCormick, F. and Gray, J. (2003) Chromosome aberrations in solid tumors. Nat. Genet., 34, 369-376.
2. Cowell, J. (1982) Double minutes and homogeneously staining regions. Annu. Rev. Genet., 16, 21-59.
3. Desper, R., Jiang, F., Kallioniemi, O.P., Moch, H., Papadimitriou, C.H. and Schaffer, A.A. (1999) Inferring tree models for oncogenesis from comparative genome hybridization data. J. Comput. Biol., 6, 37-51.
4. Garey, M. and Johnson, S. (1979) Computers and Intractability: A Guide to the theory of NP-completeness. W.H. Freeman, San Francisco, CA.
5. Guan, X., Meltzer, P.S., Dalton, W.S. and Trent, J.M. (1994) Identification of cryptic sites of DNA sequence amplification in human breast cancer by chromosome microdissection. Nat. Genet., 8, 155-161.
6. Heisterkamp, N., Stephenson, J.R., Groffen, J., Hansen, P.F., de Klein, A., Bartram, C.R. and Grosveld, G. (1983) Localization of the c-abl oncogene adjacent to a translocation break point in chronic myelocytic leukaemia. Nature, 306, 239-242.
7. Hodgson, G., Hager, J.H., Volik, S., Hariono, S., Wernick, M., Moore, D., Albertson, D.G., Pinkel, D., Collins, C., (2001) Genome scanning with array CGH delineates regional alterations in mouse islet carcinomas. Nat. Genet., 29, 459-464.
8. Kallioniemi, A., Kallioniemi, O.P., Sudar, D., Rutouitz, D., Gray, J.W., Waldman, F. and Pinkal, D. (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science, 258, 818-821.
9. Kytola, S., Rummukainen, J., Nordgren, A., Karhu, R., Farnebo, F., Isola, J., and Larsson, C. (2000) Chromosomal alterations in 15 breast cancer cell lines by comparative genomic hybridization and spectral karyotyping. Genes Chrom. Cancer, 28, 308-317.
10. Loeb, L., Loeb, K. and Anderson, J. (2003) Multiple mutations and cancer. Proc. Natl Acad. Sci., USA, 100, 776-781.
11. Pevzner, P. (2000) Computational Molecular Biology: An Algorithmic Approach. MIT Press, Cambridge, MA.
12. Pevzner, P. and Tesler, G. (2003) Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Res., 13, 37-45.
13. Raphael, B.J., Volik, S., Collins, C. and Pevzner, P.A. (2003) Reconstructing tumor genome architectures. Bioinformatics, 19 (Suppl. 2), II162-II171.
14. Schröck, E., du Manoir, S., Veldman, T., Schoell, B., Wienberg, J., Ferquson-Smith, M.A., Ning, Y., Ledbetter, D.H., Bar-Am, I., Soenksen, D., Garini, Y. and Ried, T. (1996) Multicolor spectral karyotyping of human chromosomes. Science, 273, 494-497.
15. Snijders, A., Nowak, N., Seqraves, R., Blackwood, S., Brown, N., Conroy, J., Hamilton, G., Hindle, A.K., (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat. Genet., 29, 263-264.
16. Toledo, F., Le Roscouet, D., Buttin, G. and Debatisse, M. (1992) Co-amplified markers alternate in megabase long chromosomal inverted repeats and cluster independently in interphase nuclei at early steps of mammalian gene amplification. EMBO J., 11, 2665-2673.
17. Vogelstein, B., Fearon, E.R., Hamilton, S.R., Kern, S.E., Preisinger, A.C., Leppert, M., Nakamura, Y., White, R., Smits, A.M.M. and Bos, J. (1988) Genetic alterations during colorectal-tumor development. N. Engl. J. Med., 319, 525-532.
18. Volik, S. Shao, S., Chin, K., Brebner, J.H., Herndon, D.R., Jao, Q., Kowbel, D., Huang, G., Lapuk, A., Kuo, W.-L. et al. (2003) End-sequence profiling: sequence-based analysis of aberrant genomes. Proc. Natl Acad. Sci., USA, 100, 7696-7701.
19. Von Hoff, D.D., Forseth, B., Clare, C.N., Hansen, K.E. and Van Deuanter, D. (1990) Double minutes arise from circular extra-chromosomal DNA intermediates which integrate into chromosomal sites in human HL-60 leukemia cells. J. Clin. Invest., 85, 1887-1895.
20. Von Hoff, D.D., McGill, J.R., Forseth, B.J., Davidson, K.K., Bradley, T.P., Van Devanter, D.R. and Wahl, G.M. (1992) Elimination of extrachromosomally amplified MYC genes from human tumor cells reduces their tumorigenicity. Proc. Natl Acad. Sci., USA, 89, 8165-8169.