Inferring tree models for oncogenesis from comparative genome hybridization data

Journal of Computational Biology

Volumn 6, Issue 1, 1999, Pages 37-51

  Desper, Richard ^a   Jiang, Feng ^b   Kallioniemi, Olli P ^c   Moch, Holger ^b   Papadimitriou, Christos H ^d   Schäffer, Alejandro A ^c,e  

^a RUTGERS UNIVERSITY   (United States)

^b UNIVERSITY OF BASEL   (Switzerland)

^c NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Algorithms; Branching; Cancer genetics; Comparative genome hybridization; Renal cancer; Tree inference

Indexed keywords

ALGORITHM; ARTICLE; CANCER DIAGNOSIS; CANCER GENETICS; CARCINOGENESIS; CELL DEATH; CHROMOSOME ABERRATION; CHROMOSOME LOSS; CYTOGENETICS; GENE ACTIVATION; KIDNEY CANCER; MODEL; PRIORITY JOURNAL; TUMOR SUPPRESSOR GENE;

EID: 0032894615     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.1999.6.37     Document Type: Article

References (35)

1. Alon, N., Spencer, J.H., and Erdös, P. 1992. The Probabilistic Method. John Wiley & Sons, New York.
2. Brodeur, G.M., Tsiatis, A.A., Williams, D.L., Luthardt, F.W., and Green, A.A. 1982. Statistical analysis of cytogenetic abnormalities in human cancer cells. Cancer Genet. Cytogenet. 7, 137-152.
3. Buetow, K.H., Edmonson, M.N., Shen, F.M., Chen, G.C., London, W.T., and McGlynn, K.A. 1998. Identification of molecular heterogeneity in HCC using STRPs and tree-building algorithms. Am. J. Hum. Genet. 63, A336 (abst).
4. Cavender, J.A. 1978. Taxonomy with confidence. Math. Biosci. 40, 271-280.
5. Chu, Y.J., and Liu, T.H. 1965. On the shortest arborescence of a directed graph. Sci. Sinica 14, 1396-1400.
6. Edmonds, J. 1967. Optimum branchings. J. Res. Nat. Bur. Stand. 71B, 233-240.
7. Erlandsson, R. 1998. Molecular genetics of renal cell carcinoma. Cancer Genet. Cytogenet. 104, 1-18.
8. Farris, J.S. 1973. A probability model for inferring evolutionary trees. Syst. Zool. 22, 250-256.
9. Fearon, E., and Vogelstein, B. 1990. A genetic model for colorectal tumorigenesis. Cell 61, 759-767.
10. Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27, 401-410.
11. Fill, J.A., and Pemantle, R. 1993. Percolation, first-passage percolation, and covering times for Richardson's model on the n-cube. Ann. Appl. Prob. 3, 593-629.
12. Forozan, F., Karhu, R., Kononen, J., Kallioniemi, A., and Kallioniemi, O.-P. 1997. Genome screening by comparative genome hybridization. Trends Genet. 13, 405-409.
13. Gnarra, J.R., Tory, K., Weng, Y., et al. 1994. Mutations of the VHL tumour suppressor gene in renal carcinoma. Nat. Genet. 7, 85-90.
14. Hemminki, A., Tomlinson, I., Markie, D., et al. 1997. Localization of a susceptibility locus for Peutz-Jeghers syndrome to 19p using comparative genomic hybridization and targeted linkage analysis. Nat. Genet. 15, 87-90.
15. Jiang, F., Richter, J., Schraml, P., et al. 1998. Chromosomal imbalances in papillary renal cell carcinoma: genetic differences between histological subtypes. Am. J. Pathol. 153, 1467-1473.
16. Kallioniemi, A., Kallioniemi, O.P., Sudar, D., et al. 1992. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258, 818-821.
17. Karp, R.M. 1971. A simple derivation of Edmonds' algorithm for optimum branching. Networks 1, 265-272.
18. Kuukasjärvi, T., Karhu, R., Tanner, M., et al. 1997. Genetic heterogeneity and clonal evolution underlying development of asynchronous metastasis in human breast cancer. Cancer Res. 57, 1597-1604.
19. Latif, F., Tory, K., Gnarra, J., et al. 1993. Identification of the von Hippel-Lindau disease tumor suppressor gene. Science 260, 1317-1320.
20. Moch, H., Presti, J.C., Sauter, G., et al. 1996. Genetic aberrations detected by comparative genomic hybridization are associated with clinical outcome in renal cell carcinoma. Cancer Res. 56, 27-30.
21. Moch, H., Schraml, P., Bubendorf, L., et al. 1998. Intratumoral heterogeneity of von Hippel-Lindau gene deletions in renal cell carcinoma detected by fluorescence in situ hybridization. Cancer Res. 58, 2304-2309.
22. Motzer, R.J., Bander, N.H., and Nanus, D.M. 1996. Renal cell carcinoma. N. Engl. J. Med. 335, 865-875.
23. Newton, M.A., Wu, S.-Q., and Reznikoff, C.A. 1994. Assessing the significance of chromosome-loss data: where are suppressor genes for bladder cancer? Stat. Med. 13, 839-858.
24. Neyman, J. 1971. Molecular studies of evolution: a source of novel statistical problems, 1-27. In Gupta, S.S., and Yackel, J., eds., Statistical Decision Theory and Related Topics, Academic Press, New York.
25. Nowell, P.C. 1976. The clonal evolution of tumor cell populations. Science 194, 23-28.
26. Papadimitriou, C.H., and Steiglitz, K. 1982. Combinatorial Optimization. Prentice Hall, Englewood Cliffs, NJ.
27. Richardson, D. 1973. Random growth in a tesselation. Proc. Camb. Phil. Soc. 74, 515-528.
28. Ried, T., Knutzen, R., Steinbeck, R., et al. 1996. Comparative genomic hybridization reveals a specific pattern of chromosomal gains and losses during the genesis of colorectal tumors. Genes Chromosomes Cancer 15, 234-245.
29. Schmidt, L., Duh, F.-M., Chen, F., et al. 1997. Germline and somatic mutations in the tyrosine kinase domain of the MET proto-oncogene in papillary renal carcinomas. Nat. Genet. 16, 68-73.
30. Sidhar, S.K., Clark, J., Gill, S., et al. 1996. The t(X;1)(p11.2;q21.2) translocation in papillary renal cell carcinoma fuses a novel gene PRCC to the TFE3 transcription factor gene. Hum. Mol. Genet. 5, 1333-1338.
31. Tarjan, R.E. 1977. Finding optimum branchings. Networks 7, 25-35.
32. Thrash-Bingham, C.A., Salazar, H., Freed, J.J., Greenberg, R.E., and Tartof, K.D. 1995. Genomic alterations and instabilities in renal cell carcinomas and their relationship to tumor pathology. Cancer Res. 55, 6189-6195.
33. Tirkkonen, M., Johannson, O., Agnarsson, B., et al. 1997. Distinct somatic genetic changes associated with tumor progression in carriers of BRCA1 and BRCA2 germ-line mutations. Cancer Res. 57, 1222-1227.
34. Vogelstein, B., Fearon, E., Hamilton, S., et al. 1988. Genetic alterations during colorectal-tumor development. N. Engl. J. Med. 319, 525-532.
35. Westerman, M.A.J., Wilbrink, M., and Geurts van Kessel, A. 1996. Fusion of the transcription factor TFE3 gene to a novel gene, PRCC, in t(X;1)(p11;q21)-positive papillary renal cell carcinomas. 1996. Proc. Natl. Acad. Sci. U.S.A. 93, 15294-15298.