Clonal and non-clonal chromosome aberrations and genome variation and aberration

Genome

Volumn 49, Issue 3, 2006, Pages 195-204

  Heng, Henry H Q ^a   Liu, Guo ^a   Bremer, Steven ^a   Ye, Karen J ^b   Stevens, Joshua ^a   Ye, Christine J ^a,b  

^a WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b SeeDNA Biotech Inc   (Canada)

Author keywords

Cancer evolution; Clonal chromosome aberration (CCA); Genome aberration and variation; Karyotype; Non clonal chromosome aberration (NCCA); Transitional CCA

Indexed keywords

CELL CLONE; CHROMOSOME ABERRATION; GENETIC VARIABILITY; GENETICS; GENOME; HUMAN; KARYOTYPING; NEOPLASM; SHORT SURVEY;

CHROMOSOME ABERRATIONS; CLONE CELLS; GENOME, HUMAN; HUMANS; KARYOTYPING; NEOPLASMS; VARIATION (GENETICS);

EID: 33745580375     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/g06-023     Document Type: Short Survey

References (81)

1. Albertson, D.G., Collins, C., McCormick, F., and Gray, J.W. 2003. Chromosome aberrations in solid tumors. Nat. Genet. 34: 369-376.
2. Artandi, S.E., Chang, S., Lee, S.L., Alson, S., Gottlieb, G.J., Chin, L., and DePinho, R.A. 2000. Telomere dysfunction promotes non-reciprocal translocations and epithelial cancers in mice. Nature (London), 406: 641-645.
3. Bassing, C.H., Suh, H., Ferguson, D.O., Chua, K.F., Manis, J., Eckersdorff, M., Gleason, M., Bronson, R., Lee, C., and Alt, F.W. 2003. Histone H2AX: a dosage-dependent suppressor of oncogenic translocations and tumors. Cell, 114: 359-370.
4. Becskei, A., Kaufmann, B.B., and van Oudenaarden, A. 2005. Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nat. Genet. 37: 937-944.
5. Bignell, G., Smith, R., Hunter, C., Stephens, P., Davies, H., Greenman, C. et al. 2006. Sequence analysis of the protein kinase gene family in human testicular germ-cell tumors of adolescents and adults. Genes Chromosomes Cancer, 45: 42-46.
6. Bischoff, F.Z., Yim, SO., Pathak, S., Grant, G., Siciliano, M.J., Giovanella, B.C., et al. 1990. Spontaneous abnormalities in normal fibroblasts from patients with Li-Fraumeni cancer syndrome: aneuploidy and immortalization. Cancer Res. 50: 7979-7984.
7. Bode, J., Goetze, S., Heng, H., Krawetz, S.A., and Benham, C. 2003. From DNA structure to gene expression: mediators of nuclear compartmentalization and dynamics. Chromosome Res. 11: 435-445
8. Bonassi, S., Abbondandolo, A., Camurri, L., Dal Pra, L., De Ferrari, M., Degrassi, F. et al. 1995. Are chromosome aberrations in circulating lymphocytes predictive of future cancer onset in humans? Preliminary results of an Italian cohort study. Cancer Genet. Cytogenet. 79: 133-135.
9. Bonassi, S., Znaor, A., Norppa, H., and Hagmar, L. 2004. Chromosomal aberrations and risk of cancer in humans: an epidemiologic perspective. Cytogenet. Genome Res. 104: 376-382.
10. Cahill, D.P., Kinzler, K.W., Vogelstein, B., and Lengauer, C. 1999. Genetic instability and Darwinian selection in tumours. Trends Cell Biol. 9: M57-M60.
11. Choo, K.H.A. 1997. The Centromere. Oxford University Press, Oxford, UK.
12. Claussen, U. 2005. Chromosomics. Cytogenet. Genome Res. 111: 101-106.
13. Cremer, T., and Cremer, C. 2001. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat. Rev. Genet. 2: 292-301.
14. Davies, H., Hunter, C., Smith, R., Stephens, P., Greenman, C., Bignell, G. et al. 2005. Somatic mutations of the protein kinase gene family in human lung cancer. Cancer Res. 65: 7591-7595.
15. Duesberg, P. 2005. Does aneuploidy or mutation start cancer? Science (Washington, D.C.), 307: 41.
16. Duesberg, P., Li, R., Fabarius, A., and Hehlmann, R. 2005. The chromosomal basis of cancer. Cell Oncol. 27: 293-318.
17. Egger, G., Liang, G., Aparicio, A., and Jones, P.A. 2004. Epigenetics in human disease and prospects for epigenetic therapy. Nature (London), 429: 457-463.
18. Feinberg, A.P., Ohlsson, R., and Henikoff, S. 2006. The epigenetic progenitor origin of human cancer. Nat. Rev. Genet. 7: 21-33.
19. Ferguson, D.O., and Alt, F.W. 2001. DNA double strand break repair and chromosomal translocation: lessons from animal models. Oncogene, 20: 5572-5579.
20. Ferguson, D.O., Sekiguchi, J.M., Chang, S., Frank, K.M., Gao, Y., DePinho, R.A., and Alt, F.W. 2000. The nonhomologous end-joining pathway of DNA repair is required for genomic stability and the suppression of translocations. Proc. Natl. Acad. Sci. U.S.A. 97: 6630-6633.
21. Fukasawa, K., Wiener, F., Vande Woude, G.F., and Mai, S. 1997. Genomic instability and apoptosis are frequent in p53 deficient young mice. Oncogene, 15: 1295-1302.
22. Gibbs, W.W. 2003. Untangling the roots of cancer. Sci. Am. 289: 56-65.
23. Gisselsson, D., Jonson, T., Petersen, A., Strombeck, B., Dal Cin, P., Hoglund, M. et al. 2001. Telomere dysfunction triggers extensive DNA fragmentation and evolution of complex chromosome abnormalities in human malignant tumors. Proc. Natl. Acad. Sci. U.S.A. 98: 12683-12688.
24. Hanks, S., Coleman, K., Reid, S., Plaja, A., Firth, H., Fitzpatrick, D. et al. 2004. Constitutional aneuploidy and cancer predisposi-tion caused by biallelic mutations in BUB1B. Nat. Genet. 36: 1159-1161.
25. Heng, H.H.Q. 2006a. Can cancer genome sequencing unravel the mystery of cancer?
26. Heng, H.H.Q. 2006b. Cancer progression by non-clonal chromosome aberrations.
27. Heng, H.H., and Tsui, L.C. 1998. High resolution free chromatin/DNA fiber fluorescent in situ hybridization. J. Chromatogr. A, 806: 219-229.
28. Heng, H.Q., Chen, W.Y., and Wang, Y.C. 1988. Effects of pingyanymycin on chromosomes: a possible structural basis for chromosome aberration. Mutat. Res. 199: 199-205.
29. Heng, H.H., Squire, J., and Tsui, L.C. 1992. High-resolution mapping of mammalian genes by in situ hybridization to free chromatin. Proc. Natl. Acad. Sci. U.S.A. 89: 9509-9513.
30. Heng, H.H., Tsui, L.C., and Moens, P.B. 1994. Organization of heterologous DNA inserts on the mouse meiotic chromosome core. Chromosoma, 103: 401-407.
31. Heng, H.H., Chamberlain, J.W., Shi, X.M., Spyropoulos, B., Tsui, L.C., and Moens, P.B. 1996. Regulation of meiotic chromatin loop size by chromosomal position. Proc. Natl. Acad. Sci. U.S.A. 93: 2795-2800.
32. Heng, H.H., Spyropoulos, B., and Moens, P.B. 1997. FISH technology in chromosome and genome research. Bioessays, 19: 75-84.
33. Heng, H.H., Krawetz, S.K., Lu, W., Bremer, S., Liu, G., and Ye, C.J. 2001, Re-defining the chromatin loop domain. Cytogenet. Cell Genet. 93: 155-161.
34. Heng, H.H., Ye, C.J., Yang, F., Ebrahim, S., Liu, G., Bremer, S.W., et al. 2003. Analysis of marker or complex chromosomal rearrangements present in pre- and post-natal karyotypes utilizing a combination of G-banding, spectral karyotyping and fluorescence in situ hybridization. Clin. Genet. 63: 358-367.
35. Heng, H.H., Goetze, S., Ye, C.J., Liu, G., Stevens, J.B., Bremer, S.W., Wykes, S.M., Bode, J., and Krawetz, S.A. 2004a. Chromatin loops are selectively anchored using scaffold/matrix-attachment regions. J. Cell Sci. 117: 999-1008.
36. Heng, H.H., Stevens, J., Liu, G., Bremer, S.W., and Ye, C.J. 2004b. Imaging genome abnormalities in cancer research. Cell Chromosomes, 3: 1.
37. Heng, H.H., Stevens, J., Liu, G., Bremer, S.W., Ye, J., Wang, A.Y., Tainsky, M., Reddy, P., Wu, G.-S., and Ye, C.J. 2006. Stochastic cancer progression driven by non-clonal chromosome aberrations.
38. Heppner, G.H., and Miller, F.R. 1998. The cellular basis of tumor progression. Int. Rev. Cytol. 177: 1-56.
39. Hoglund, M., Gisselsson, D., Mandahl, N., Johansson, B., Mertens, F., Mitelman, F., and Sall, T. 2001. Multivariate analyses of genomic imbalances in solid tumors reveal distinct and converging pathways of karyotypic evolution. Genes Chromosomes Cancer, 31: 156-171.
40. Hoglund, M., Gisselsson, D., Hansen, G.B., Sail, T., Mitelman, F., and Nilbert, M. 2002. Dissecting karyotypic patterns in colorectal tumors: two distinct but overlapping pathways in the adenoma-carcinoma transition. Cancer Res. 62: 5939-5946.
41. Hoglund, M., Frigyesi, A., Sail, T., Gisselsson, D., and Mitelman, F. 2005. Statistical behavior of complex cancer karyotypes. Genes Chromosomes Cancer, 42: 327-341.
42. Iafrate, A.J., Feuk, L., Rivera, M.N., Listewnik, M.L., Donahoe, P.K., Qi, Y., Scherer, S.W., and Lee, C. 2004. Detection of large-scale variation in the human genome. Nat. Genet. 36: 949-951.
43. Jabs, E.W., Tuck-Muller, C.M, Cusano, R., and Rattner, J.B. 1991. Studies of mitotic and centromeric abnormalities in Roberts syndrome: implications for a defect in the mitotic mechanism. Chromosoma, 100: 251-261.
44. Jaenisch, R., and Bird, A. 2003. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat. Genet. 33(Suppl): 245-54.
45. Lengauer, C., Kinzler, K.W., and Vogelstein, B. 1998. Genetic instabilities in human cancers. Nature (London), 396: 643-649.
46. Li, R., Hehlman, R., Sachs, R., and Duesberg, P. 2005. Chromosomal alterations cause the high rates and wide ranges of drug resistance in cancer cells. Cancer Genet. Cytogenet. 163: 44-56.
47. McClintock, B. 1940. The stability of broken ends of chromosomes in Zea mays. Genetics, 26: 234-238.
48. Mitelman, F. 2000. Recurrent chromosome aberrations in cancer. Mutat. Res. 462: 247-253.
49. Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature (London), 420: 520-562.
50. Murphy, W.J., Larkin, D.M., Everts-van der Wind, A., Bourque, G., Tesler, G., Auvil, L. et al. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science (Washington, D.C.), 309: 613-617.
51. Natarajan, A.T., and Boei, J.J. 2003. Formation of chromosome aberrations: insights from FISH. Mutat. Res. 544: 299-304.
52. Navarro, A., and Barton, N.H. 2003. Chromosomal speciation and molecular divergence - accelerated evolution in rearranged chromosomes. Science (Washington, D.C.), 300: 321-324.
53. Nowell, P.C. 1976. The clonal evolution of tumor cell populations. Science (Washington, D.C.), 194: 23-28.
54. Omori, F., Messner, H.A., Ye, C., Gronda, M.V., O'Neill, J.P., Atkins, H., and Heng, H.H. 1999. Nontargeted stable integration of recombinant adeno-associated virus into human leukemia and lymphoma cell lines as evaluated by fluorescence in situ hybridization. Hum. Gene Ther. 10: 537-543.
55. Osborne, C.S., Chakalova, L., Brown, K.E., Carter, D., Horton, A., Debrand, E. et al. 2004. Active genes dynamically colocalize to shared sites of ongoing transcription. Nat. Genet. 36: 1065-1071.
56. Rajagopalan, H., and Lengauer, C. 2004. Aneuploidy and cancer. Nature (London), 432: 338-341.
57. Romanov, S.R., Kozakiewicz, B.K., Holst, C.R., Stampfer, M.R., Haupt, L.M., and Tlsty, T.D. 2001. Normal human mammary epithelial cells spontaneously escape senescence and acquire genomic changes. Nature (London), 409: 633-637.
58. Rowley, J.D. 2001. Chromosome translocations: dangerous liaisons revisited. Nat. Rev. Cancer, 1: 245-250.
59. Schrock, E., du Manoir, S., Veldman, T., Schoell, B., Wienberg, J., Ferguson-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 (Washington, D.C.), 273: 494-497.
60. Schroeder, T.M., and German, J. 1974. Bloom's syndrome and Fanconi's anemia: demonstration of two distinctive patterns of chromosome disruption and rearrangement. Humangenetik, 25: 299-306.
61. Sharpless, N.E., Ferguson, D.O., O'Hagan, R.C., Castrillon, D.H., Lee, C., Farazi, P.A. et al. 2001. Impaired nonhomologous end-joining provokes soft tissue sarcomas harboring chromosomal translocations, amplifications, and deletions. Mol. Cell, 8: 1187-1196.
62. Shen, K.C., Heng, H., Lu, S., Wang, Y., Liu, G., Deng, C.X., Brooks, S.C., and Wang, Y.A. 2005. ATM and p21 cooperate to suppress aneuploidy and subsequent tumor development. Cancer Res. 65: 8747-8753.
63. Shi, Q., and King, R.W. 2005. Chromosome nondisjunction yields tetraploid rather than aneuploid cells in human cell lines. Nature (London), 437: 1038-1042.
64. Smith, L., Plug, A., and Thayer, M. 2001. Delayed replication timing leads to delayed mitotic chromosome condensation and chromosomal instability of chromosome translocations. Proc. Natl. Acad. Sci. U.S.A. 98: 13300-13305.
65. Speicher, M.R., Gwyn Ballard, S., and Ward, D.C. 1996. Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat. Genet. 12: 368-375.
66. Spitz, M.R, and Hsu, T.C. 1994. Mutagen sensitivity as a marker of cancer risk. Cancer Detect. Prev. 18: 299-303.
67. Squire, J.A., Marrano, P., and Kolomietz, E. 2002. FISH in clinical cytogenetics. In FISH, practical approach. Edited by B. Beatty, S. Mai, and J. Squire. Oxford University Press, New York, N.Y. pp. 183-202.
68. Stephens, P., Edkins, S., Davies, H., Greenman, C., Cox, C., Hunter, C. et al. 2005. A screen of the complete protein kinase gene family identifies diverse patterns of somatic mutations in human breast cancer. Nat. Genet. 37: 590-592.
69. Stevens, J.B., Savasan, S., Liu, G., Bremer, S., Atanasovski, M., Xu, W. et al. 2004. Cell death by chromosome elimination: Characterization of drug induced chromosomal fragmentation. ASHG 2004 Annual Meeting, program number 326.
70. Tlsty, T.D., Crawford, Y.G., Holst, C.R., Fordyce, C.A., Zhang, J., McDermott, K., Kozakiewicz, K., and Gauthier, M.L. 2004. Genetic and epigenetic changes in mammary epithelial cells may mimic early events in carcinogenesis. J. Mamm. Gland Biol. Neoplasia, 9: 263-274.
71. Trask, B.J. 2002. Human cytogenetics: 46 chromosomes, 46 years and counting. Nat. Rev. Genet. 3: 769-778.
72. van Ommen, G.J. 2005. Frequency of new copy number variation in humans. Nat. Genet. 37: 333-334.
73. Varmuza, S. 2003. Epigenetics and the renaissance of heresy. Genome, 46: 963-967.
74. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G. et al. 2001. The sequence of the human genome. Science (Washington, D.C.), 291: 1304-1351.
75. Voullaire, L.E., Slater, H.R., Petrovic, V., and Choo, K.H. 1993. A functional marker centromere with no detectable alpha-satellite, satellite III, or CENP-B protein: activation of a latent centromere? Am. J. Hum. Genet. 52: 1153-1163.
76. Wu, X., Zheng, Y.L., and Hsu, T.C. 2005. Mutagen-induced chromatid breakage as a marker of cancer risk. Methods Mol. Biol. 291: 59-67.
77. Xu, X., Wagner, K.U., Larson, D., Weaver, Z., Li, C., and Reid, T. et al. 1999. Conditional mutation of Brca1 in mammary epithelial cells results in blunted ductal morphogenesis and tumour formation. Nat. Genet. 22: 37-43.
78. Yang, F., Fu, B., O'Brien, P.C., Robinson, T.J., Ryder, O.A., and Ferguson-Smith, M.A. 2003. Karyotypic relationships of horses and zebras: results of cross-species chromosome painting. Cytogenet. Genome Res. 102: 235-243.
79. Ye, C.J., Lu, W., Liu, G., Bremer, S.W., Wang, Y.A., Moens, P. et al. 2001. The combination of SKY and specific loci detection with FISH or immunostaining. Cytogenet. Cell Genet. 93: 195-202.
80. Ye, C.J., Stevens, J., Liu, G., Ye, J., Yang, F., Bremer, S.W., and Heng, H.H.Q. 2006. Combined Multicolor-FISH and Immunostaining. Cytogenet. Genome Res. In press.
81. Yu, V.P., Koehler, M., Steinlein, C., Schmid, M., Hanakahi, L.A., van Gool, A.J. et al. 2000. Gross chromosomal rearrangements and genetic exchange between nonhomologous chromosomes following BRCA2 inactivation. Genes Dev. 14: 1400-1406.