Chromosome abnormalities in ovarian adenocarcinoma: III. Using breakpoint data to infer and test mathematical models for oncogenesis

Genes Chromosomes and Cancer

Volumn 28, Issue 1, 2000, Pages 106-120

  Simon, Richard ^a   Desper, Richard ^b   Papadimitriou, Christos H ^c   Peng, Amy ^d   Alberts, David S ^e   Taetle, Raymond ^e   Trent, Jeffrey M ^f   Schäffer, Alejandro A ^g  

^a NATIONAL CANCER INSTITUTE   (United States)

^b GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d EMMES CORPORATION   (United States)

^e UNIVERSITY OF ARIZONA   (United States)

^f NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^g NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; CANCER SURVIVAL; CARCINOGENESIS; CHROMOSOME ABERRATION; CHROMOSOME BREAKAGE; FEMALE; HUMAN; HUMAN TISSUE; MATHEMATICAL MODEL; OVARY ADENOCARCINOMA; PHYLOGENY; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; STATISTICS; TUMOR GROWTH;

ADENOCARCINOMA; CELL TRANSFORMATION, NEOPLASTIC; CHROMOSOME ABERRATIONS; CHROMOSOME BREAKAGE; CHROMOSOME DISORDERS; FEMALE; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; ONCOGENES; OVARIAN NEOPLASMS; PHYLOGENY; RANDOM ALLOCATION; STATISTICS, NONPARAMETRIC; SURVIVAL RATE;

EID: 0034110066     PISSN: 10452257     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1098-2264(200005)28:1<106::AID-GCC13>3.0.CO;2-S     Document Type: Article

References (30)

1. Barthélemy J-P, Guénoche A. 1991. Trees and proximity representations. New York: Wiley.
2. Becker RA, Chambers JM, Wilks AR. 1988. The New S Language. Pacific Grove, CA: Wadsworth and Brooks/Cole.
3. Brodeur GM, Tsiatis AA, Williams DL, Luthardt FW, Green AA. 1982. Statistical analysis of cytogenetic abnormalities in human cancer cells. Cancer Genet Cytogenet 7:137-152.
4. Chu YJ, Liu TH. 1965. On the shortest arborescence of a directed graph. Sci Sin 14:1396-1400.
5. Daniel A. 1985. The size of prometaphase chromosome segments. Clin Genet 28:216-224.
6. DcRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen V, Su YA, Trent JM. 1996. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nature Genet 14:457-460.
7. Desper R, Jiang F, Kallioniemi OP, Moch H, Papadimitriou CH, Schäffer AA. 1999. Inferring tree models for oncogenesis from comparative genomic hybridization data. J Comp Biol 6:37-51.
8. Desper R, Jiang F, Kallioniemi OP, Moch H, Papadimitriou CH, Schäffer AA. Distance-based reconstruction of tree models for oncogenesis J Comp Biol (in press).
9. Edmonds J. 1967. Optimum branchings. J Res Nat Bur Stand 71B: 233-240.
10. Faraggi D, Simon R. 1997. Large sample Bayesian inference on the parameters of the proportional hazard models. Stat Med 16:2573-2585.
11. Fearon E, Vogelstein B. 1990. A genetic model for colorectal tumorigencsis. Cell 61:759-767.
12. Felsenstein J. 1989. PHYLIP - phylogeny inference package (version 3.2). Cladistics 5:164-166. (See also http://evolution.genetic-s.washington.edu/phylip.html).
13. Fitch WM, Margoliash E. 1967. Construction of phylogenetic trees. Science 155:279-284.
14. ISCN. 1995. International system for human cytogenetic nomenclature. Mitelman F, editor. Basel: S. Karger.
15. Jenkins RB, Bartelt D Jr, Stalboerger P, Persons D, Dahl RJ, Podratz K, Keeney G, Hartmann L. 1993. Cytogenetic studies of epithelial ovarian carcinoma. Cancer Genet Cytogenet 71:76-86.
16. Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D. 1992. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258: 818-821.
17. Karp RM. 1971. A simple derivation of Edmonds' algorithm for optimum branching. Networks 1:265-272.
18. Kuukasjärvi T, Karhu R, Tanner M, Kähkönen M, Schäffer A, Nupponnen N, Pennanen S, Kallioniemi A, Kallioniemi OP, Isola J. 1997. Genetic heterogeneity and clonal evolution underlying development of asynchronous metastasis in human breast cancer. Cancer Res 57:1597-1604.
19. Morrison DF. 1967. Multivariate statistical methods. New York: McGraw-Hill.
20. Newton MA, Wu SQ, Reznikoff CA. 1994. Assessing the significance of chromosome-loss data: where are suppressor genes for bladder cancer. Stat Med 13:839-858.
21. Pciovic T, Heim S, Mandahl N, Baldetorp B, Elmfors B, Flodérus UM, Furgyik S, Helm G, Himmelmann A, Willén H, Mitelman F. 1992. Chromosome aberrations in 35 primary ovarian carcinomas. Genes Chromosomes Cancer 4:58-68.
22. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-424.
23. Swofford DL, Olsen GJ. 1990. Phylogeny reconstruction. In: Hillis DM, Moritz C, editors. Molecular systematics. Sunderland, MA: Sinauer Associates, Inc. p 411-501.
24. Taetle R, Aickin M, Yang JM, Panda L, Emerson J, Roe D, Adair L, Thompson F, Liu Y, Wisner L, Davis JR, Trent J, Alberts DS. 1999a. Chromosome abnormalities in ovarian adenocarcinoma: I. Non-random chromosome abnormalities from 244 cases. Genes Chromosomes Cancer 25:290-300.
25. Taetle R, Aickin M, Panda L, Emerson J, Roe D, Thompson F, Davis J, Trent J, Alberts D. 1999b. Chromosome abnormalities in ovarian adenocarcinoma: II. Prognostic impact of nonrandom chromosome abnormalities in 244 cases. Genes Chromosomes Cancer 25:46-52.
26. Tarjan RE. 1977. Finding optimum branchings. Networks 7:25-35.
27. Thompson FH, Liu Y, Emerson J, Weinstein R, Makar R, Trent JM, Taetle R, Alberts DS. 1994. Simple numeric abnormalities as primary karyotype changes in ovarian carcinoma. Genes Chromosomes Cancer 10:262-266.
28. Thompson FH, Taetle R, Trent JM, Liu V, Massey-Brown K, Scott KM, Weinstein RS, Emerson JC, Alberts DS, Nelson MA. 1997. Band 1p36 abnormalities and t(1; 17) in ovarian carcinoma. Cancer Genet Cytogenet 96:106-110.
29. Vogelstein B, Fcaron E, Hamilton S, Kern S, Preisinger A, Leppert M, Nakamura Y, White R, Smits A, Bos J. 1988. Genetic alterations during colorectal-tumor development. N Engl J Med 319: 525-532.
30. Zhang L, Zhou W, Velculescu V, Kern S, Hruban R, Hamilton S, Vogelstein B, Kinzler K. 1997. Gene expression profiles in normal and cancer cells. Science 276:1268-1272.