Cancer genome sequencing: The challenges ahead

BioEssays

Volumn 29, Issue 8, 2007, Pages 783-794

  Heng, Henry H Q ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

IMATINIB;

CANCER GROWTH; CANCER RESEARCH; CARCINOGENESIS; CHROMOSOME ABERRATION; CHROMOSOME ANALYSIS; CHRONIC MYELOID LEUKEMIA; DNA REPAIR; ENVIRONMENTAL FACTOR; EPIGENETICS; GENE EXPRESSION; GENE MUTATION; GENE SEQUENCE; GENETIC HETEROGENEITY; GENETIC VARIABILITY; GENOMIC INSTABILITY; NONHUMAN; REVIEW; SOLID TUMOR;

CHROMOSOME ABERRATIONS; DISEASE PROGRESSION; ENVIRONMENT; EPIGENESIS, GENETIC; GENES, NEOPLASM; GENOME, HUMAN; HUMANS; MODELS, BIOLOGICAL; MUTATION; NEOPLASMS; RESEARCH DESIGN; SEQUENCE ANALYSIS, DNA;

EID: 34547641984     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/bies.20610     Document Type: Review

References (91)

1. Garber K. 2005. Human cancer genome project moving forward despite some doubts in community. J Natl Cancer Inst 97:1322-1324.
2. Collins FS, Barker AD. 2007. Mapping the cancer genome. Pinpointing the genes involved in cancer will help chart a new course across the complex landscape of human malignancies. Sci Am 296:50-57.
3. Vogelstein B, Kinzler KW. 2004. Cancer genes and the pathways they control. Nature Med 10:789-799.
4. Sjoblom T, et al. 2006. The consensus coding sequences of human breast and colorectal cancers. Science 314:268-274.
5. Vogelstein B, Kinzler KW. 1993. The multistep nature of cancer. Trends Genet 9:138-141.
6. Heng HH, Bremer SW, Stevens J, Ye KJ, Miller F, et al. 2006. Cancer progression by non-clonal chromosome aberrations. J Cell Biochem 98:1424-1435.
7. Hahn WC, Weinberg RA. 2002. Modelling the molecular circuitry of cancer. Nat Rev Cancer 2:331-341.
8. Esteller M. 2006. Epigenetics provides a new generation of oncogenes and tumor suppressor genes. Br J Cancer 94:179-183.
9. Miklos GL. 2005. The human cancer genome project - one more misstep in the war on cancer. Nature Biotech 23:535-537.
10. Crespi B, Summers K. 2005. Evolutionary biology of cancer. Trends Ecol Evol 20:545-552.
11. Heng HH, et al. 2006. Stochastic cancer progression driven by non-clonal chromosome aberrations. J Cell Physiol 208:461-472.
12. Merlo LM, Pepper JW, Reid BJ, Maley CC. 2006. Cancer as an evolutionary and ecological process. Nat Rev Cancer 6:924-935.
13. Nowell PC. 1976. The clonal evolution of tumor cell populations. Science 194:23-28.
14. Rowley JD. 1998. The critical role of chromosome translocations in human leukemias. Annu Rev Genet 32:495-519.
15. Johansson B, Fioretos T, Mitelman F. 2002. Cytogenetic and molecular genetic evolution of chronic myeloid leukemia. Acta Haematol 107:76-94.
16. Fearon ER. Vogelstein, B. 1990. A genetic model for colorectal tumorigenesis. Cell 61:759-767.
17. Albertson DG, et al. 2003. Chromosome aberrations in solid tumors. Nat. Genet 34:369-376.
18. Heng HH, et al. 2006. Clonal and non clonal chromosome aberrations and genome variation/aberration. Genome 49:195-204.
19. Heppner HG. 1984. Tumor heterogeneity. Cancer Res 44:2259-2265.
20. Ye C, et al. 2007. The dynamics of cancer chromosomes and genomes. Cytogenet Genome Res (in press).
21. Foulds L. 1975. Neoplastic Development, Vol. 1 Academic Press, New York.
22. Mitelman F, Johansson B, Mertens F. 2007. The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer 7:233-245.
23. Klein CA, et al. 2002. Genetic heterogeneity of single disseminated tumour cells in minimal residual cancer. Lancet 360:683-689.
24. Greenman C, et al. 2007. Patterns of somatic mutation in human cancer genome. Nature 446:153-158.
25. Sharpless NE, et al. 2001. Impaired nonhomologous end-joining provokes soft tissue sarcomas harboring chromosomal translocations, amplifications, and deletions. Mol Cell 8:1187-1196.
26. Czene K, Lichtenstein P, Hemminki K. 2002. Environmental and heritable causes of cancer among 9.6 million individuals in the Swedish Family-Cancer Database. Int J Cancer 99:260-266.
27. Frank SA, Nowak MA. 2004. Problems of somatic mutation and cancer. BioEssays 26:291-299.
28. Heng H, et al. 2007. Hematologic and solid tumors: differential patterns of cancer evolution. (Submitted).
29. Deininger M, Buchdunger E, Druker BJ. 2005. The development of imatinib as a therapeutic agent for chronic myeloid leukemia. Blood 105:2640-2653.
30. Druker BJ, et al. 2007. Five-year follow-up of patients receiving imatinib for chronic myeloid leukemia. N Engl J Med 355:2408-2417.
31. Gould SJ. 1989. Wonderful Life: The Burgess Shale and the nature of history, Penguin Books.
32. Heng HH, et al. 2004. Imaging genome abnormalities in cancer research. Cell & Chromosomes 3:1.
33. Bielas JH, et al. 2006. Human cancers express a mutator phenotype. Proc Natl Acad Sci USA 103:18238-18242.
34. Klein CA. 2006. Random mutations, selected mutations: a PIN opens the door to new genetic landscapes. Proc Natl Acad Sci USA 103:18033-18034.
35. Akagi T, Sasai K, Hanafusa H. 2003. Refractory nature of normal human diploid fibroblasts with respect to oncogene-mediated transformation. Proc Natl Acad Sci USA 100:13567-13572.
36. Hahn WC, et al. 1999. Creation of human tumour cells with defined genetic elements. Nature 400:464-468.
37. Vogelstein B, Kinzler KW. 2004. Cancer genes and the pathways they control. Nat Med 10:789-799.
38. Heppner GH. 1993. Cancer cell societies and tumor progression. Stem Cells 11:199-203.
39. Duesberg P, Li R, Fabarius A, Hehlmann R. 2005. The chromosomal basis of cancer. Cell Oncol 27:293-318.
40. Soto AM, Sonnenschein C. 2004. The somatic mutation theory of cancer: growing problems with paradigm? BioEssays 26:1097-1107.
41. Capp JP. 2005. Stochastic gene expression, disruption of tissue averaging effects and cancer as a disease of development. BioEssays 27:1277-1285.
42. Gibbs WW. 2003. Untangling the roots of cancer. Scientific American 289:56-65.
43. Feinberg AP, Ohlsson R, Henikoff S. 2006. The epigenetic progenitor origin of human cancer. Nat Rev Genet 7:21-33.
44. Atkin NB, Baker MC. 1990. Are human cancers ever diploid or often trisomic? Conflicting evidence from direct preparation and cultures. Cytogenet Cell Genet 53:58-60.
45. Lengauer C, Kinzler KW, Vagelstein B. 1998. Genetic instabilities in human cancers. Nature 396:643-649.
46. Bignell G, 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.
47. Spitz F, Gonzale F, Duboule D. 2006. A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell 113:405-417.
48. Navarro A, Barton NH. 2003. Chromosomal speciation and molecular divergence-accelerated evolution in rearranged chromosomes. Science 300:321-324.
49. Wilson AC, Sarich VM, Maxson LR. 1974. The importance of gene rearrangement in evolution: evidence from studies on Rates of chromosomal, protein, and anatomical evolution. PNAS 71:3028-3030.
50. Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562.
51. Venter JC, et al. 2001. The sequence of the human genome. Science 291:1304-1351.
52. Feuk L, Carson AR, Scherer SW. 2006. Structural variation in the human genome. Nat Rev Genet 7:85097.
53. Redon R, et al. 2006. Global variation in copy number in the human genome. Nature 444:444-454.
54. Boveri T. 1902. On Multipolar Mitosis as a Means of Analysis of the Cell Nucleus. Verhandlungen der physicalisch-medizinischen Gesselschaft zu Würzburg. Neu Folge 35:67-90.
55. Stephens P, 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.
56. Davies H, et al. 2005. Somatic mutations of the protein kinase gene family in human lung cancer. Cancer Res 65:7591-7595.
57. Jones PA, Baylin SB. 2002. The fundamental role of epigenetic events in cancer. Nat Rev Genet 3:415-428.
58. Jaffe LF. 2005. A calcium-based theory of carcinogenesis. Advances in cancer research. P231-263.
59. Fraga MF, et al. 2005. Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nat Genet 37:391-400.
60. Tlsty TD, et al. 2004. Genetic and epigenetic changes in mammary epithelial cells may mimic early events in carcinogenesis. J Mammary Gland Biol Neoplasia 9:263-274.
61. Jones PA. 2005. Overview of cancer epigenetics. Semin Hematol 42:S3-8.
62. Chung LW, Baseman A, Assikis V, Zhau HE. 2005. Molecular insights into prostate cancer progression: the missing link of tumor microenvironment. J Urol 173:10-20.
63. Pathak S, et al. 1997. Can cancer cells transformnormal host cells into malignant cells? Br J Cancer 76:1134.
64. Hochedlinger K, et al. 2004. Reprogramming of a melanoma genome by nuclear transplantation. Genes & Development 18:1875-1885.
65. Illmensee K, Mintz B. 1976. Totipotency and normal differentiation of single teratocarcinoma cells cloned by injection into blastocysts. Proc Nat Acad Sci USA 73:549-553.
66. Loi P, et al. 2001. Genetic rescue of an endangered mammal by cross-species nuclear transfer using post-mortem somatic cells. Nat Biotechnol 19:962-964.
67. Woods GL, et al. 2003. A mule cloned from fetal cells by nuclear transfer. Science 301:1063.
68. Polyak K, Hahn, WC. 2005. Roots and stems: stem cells in cancer. Nature Med 11:296-300.
69. Chin L, DePinho RA. 2000. Flipping the oncogene switch: illumination of tumor maintenance and regression. Trends Genet 16:147-150.
70. Gilbert PX, Harris H. 1988. The role of the ras oncogene in the formation of tumors. J Cell Sci 90:433-446.
71. Felsher DW, Bishop JM. 1999. Transient excess of MYC activity can elicit genomic instability and tumorigenesis. Proc Natl Acad Sci USA 96:3940-3944.
72. Worsham MJ, et al. 2006. High-resolution mapping of molecular events associated with immortalization, transformation, and progression to breast cancer in the MCF10 model. Breast Cancer Res Treat 96:177-186.
73. Rubin H. 2005. Degrees and kinds of selection in spontaneous neoplastic transformation: An operational analysis. Proc Natl Acad Sci USA 102:9276-9281.
74. Maley CC, et al. 2006. Genetic clonal diversity prediects progression to esophageal adenocarcinoma. Nat Genet 38:402-403.
75. Rubin H. 2006. What keeps cells in tissues behaving normally in the face of myriad mutations? Bioessays. 28:515-524.
76. Fidler IJ. 2003. The pathogenesis of cancer metastasis: the 'seed and soil' hypothesis revisited. Nat Rev Cancer 3:453-458.
77. Nelson CM, Bissell MJ. 2006. Of extracellular matrix, scaffolds, and signling: tissue architecture regulates development, homeostasis and cancer. Annu. Rev. Cell Dev Biol 22:287-309.
78. Coussens LM, Werb Z. 2002. Inflammation and cancer. Nature 420:860-867.
79. Barak Y. 2006. The immune system and happiness. Autoimmunity Reviews 5:523-527.
80. Pedersen BK, Hoffman-Goetz L. 2000. Exercise and the immune system: regulation, integration, and adaptation. Physiological Reviews 80:1055-1081.
81. Gatenby RA, Gillies RJ. 2004. Why do cancer have high aerobic glycolysis? Nat Rev Cancer 4:891-899.
82. Radisky DC, et al. 2006. Radb and reactive oxygene species mediate MMP-3-induced EMT and genomic instability. Nature 436:123-127.
83. Hussain SP, Hofseth LJ, Harris CC. 2003. Radical causes of cancer. Nat Rev Cancer 3:276-285.
84. Harris H. 2005. A long view of fashions in cancer research. BioEssays 27:833-838.
85. Ferres-Marco D, et al. 2006. Epigenetic silencers and Notch collaborate to promote malignant tumours by Rb silencing. Nature 439:430-436.
86. Flanagan JM. 2007. Host epigenetic modifications by oncogenic viruses. Br J Can 96:183-188.
87. Glazier A. 2006. Cure: Scientific, social and organizational requirements for the specific cure of cancer. Newton, MA: A Glazier
88. Breivik J. 2005. The evolutionary origin of genetic instability in cancer development. Seminars in Cancer Biology 15:51-60.
89. Bartos JD, et al. 2004. Genomic heterogeneity and instability in colorectal cancer: spectral karyotyping, glutathione transferase-MI and ras. Mutat Res 568:283-292.
90. Mitelman F. 2006. 50,000 tumors, 40,000 aberrations, and 300 fusion genes: how much remains? 50 years of 46 human chromosomes: progress in cytogenetics, NCI, NIH. USA.
91. Heng HH. 2007. Elimination of altered karyotypes by sexual reproduction preserves species identity. Genome 50:517-524.