Development of a phylogenetic tree model to investigate the role of genetic mutations in endometrial tumors

Oncology Reports

Volumn 25, Issue 5, 2011, Pages 1447-1454

  Zhang, Guoyi ^a   Beck, Brandon B ^c   Luo, Wentao ^b   Wu, Fan ^c   Kingsmore, Stephen F ^d   Dai, Donghai ^c  

^a UNIVERSITY OF NEW MEXICO   (United States)

^b UNIVERSITY OF NEW MEXICO SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF IOWA HEALTH CARE   (United States)

^d NATIONAL CENTER FOR GENOME RESOURCES   (United States)

Author keywords

Endometrial cancer; Genetic mutations; Phylogenetic analysis

Indexed keywords

TRANSCRIPTOME;

ADULT; ARTICLE; CARCINOGENESIS; CELL COUNT; CELL PROLIFERATION; CONTROLLED STUDY; ENDOMETRIUM TUMOR; FEMALE; GENE MUTATION; GENETIC SCREENING; GENOME ANALYSIS; HUMAN; HUMAN CELL; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; MUTATIONAL ANALYSIS; PHYLOGENETIC TREE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SOMATIC MUTATION; TUMOR CELL;

ADULT; COMPUTATIONAL BIOLOGY; ENDOMETRIAL NEOPLASMS; FEMALE; GENETIC HETEROGENEITY; HUMANS; MODELS, GENETIC; MUTATION; PHYLOGENY; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION, GENETIC;

EID: 79952374924     PISSN: 1021335X     EISSN: 17912431     Source Type: Journal    
DOI: 10.3892/or.2011.1186     Document Type: Article

References (22)

1. Vogelstein B, Fearon ER, Hamilton SR, Kern SE, Preisinger AC, Leppert M, Nakamura Y, White R, Smits AM and Bos JL: Genetic alterations during colorectal-tumor development. N Engl J Med 319: 525-532, 1988.
2. Fearon ER and Vogelstein B: A genetic model for colorectal tumorigenesis. Cell 61: 759-767, 1990.
3. Fearon ER, Hamilton SR and Vogelstein B: Clonal analysis of human colorectal tumors. Science 238: 193-197, 1987.
4. Fialkow PJ, Gartler SM and Yoshida A: Clonal origin of chronic myelocytic leukemia in man. Proc Natl Acad Sci USA 58: 1468-1471, 1967.
5. Weinberg RA: The Biology of Cancer. Garland Science, New York, NY, 2007.
6. Jones S, Chen WD, Parmigiani G, Diehl F, Beerenwinkel N, Antal T, Traulsen A, Nowak MA, Siegel C, Velculescu VE, Kinzler KW, Vogelstein B, Willis J and Markowitz SD: Comparative lesion sequencing provides insights into tumor evolution. Proc Natl Acad Sci USA 105: 4283-4288, 2008. (Pubitemid 351754372)
7. Sjoblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, Mandelker D, Leary RJ, Ptak J, Silliman N, Szabo S, Buckhaults P, Farrell C, Meeh P, Markowitz SD, Willis J, Dawson D, Willson JK, Gazdar AF, Hartigan J, Wu L, Liu C, Parmigiani G, Park BH, Bachman KE, Papadopoulos N, Vogelstein B, Kinzler KW and Velculescu VE: The consensus coding sequences of human breast and colorectal cancers. Science 314:268-274, 2006. (Pubitemid 44571966)
8. Wood LD, Parsons DW, Jones S, Lin J, Sjoblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, Nikolsky Y, Karchin R, Wilson PA, Kaminker JS, Zhang Z, Croshaw R, Willis J, Dawson D, Shipitsin M, Willson JK, Sukumar S, Polyak K, Park BH, Pethiyagoda CL, Pant PV, Ballinger DG, Sparks AB, Hartigan J, Smith DR, Suh E, Papadopoulos N, Buckhaults P, Markowitz SD, Parmigiani G, Kinzler KW, Velculescu VE and Vogelstein B: The genomic landscapes of human breast and colorectal cancers. Science 318: 1108, 2007.
9. Parsons DW, Jones S, Zhang X, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Siu IM, Gallia GL, Olivi A, McLendon R, Rasheed BA, Keir S, Nikolskaya T, Nikolsky Y, Busam DA, Tekleab H, Diaz LA Jr, Hartigan J, Smith DR, Strausberg RL, Marie SK, Shinjo SM, Yan H, Riggins GJ, Bigner DD, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE and Kinzler KW: An integrated genomic analysis of human glioblastoma multiforme. Science 321: 1807-1812, 2008.
10. Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Kamiyama H, Jimeno A, Hong SM, Fu B, Lin MT, Calhoun ES, Kamiyama M, Walter K, Nikolskaya T, Nikolsky Y, Hartigan J, Smith DR, Hidalgo M, Leach SD, Klein AP, Jaffee EM, Goggins M, Maitra A, Iacobuzio-Donahue C, Eshleman JR, Kern SE, Hraban RH, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE and Kinzler KW: Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 321: 1801-1806, 2008.
11. Sugarbaker DJ, Richards WG, Gordon GJ, Dong L, De Rienzo A, Maulik G, Glickman JN, Chirieac LR, Hartman ML, Taillon BE, Du L, Bouffard P, Kingsmore SF, Miller NA, Farmer AD, Jensen RV, Gullans SR and Bueno R: Transcriptome sequencing of malignant pleural mesothelioma tumors. Proc Natl Acad Sci USA 105: 3521-3526, 2008. (Pubitemid 351723585)
12. Cancer Genome Atlas Research Network: Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455: 1061-1068, 2008.
13. Shah S, Pishvaian MJ, Easwaran V, Brown PH and Byers SW: The role of Cadherin, beta-catenin, and AP-1 in retinoid-regulated carcinoma cell differentiation and proliferation. J Biol Chem 277: 25313-25322, 2002. (Pubitemid 34951841)
14. American Cancer Society: Cancer Facts and Figures. American Cancer Society, 2010.
15. Mudge J, Miller NA, Khrebtukova I, Lindquist IE, May GD, Huntley JJ, Luo S, Zhang L, van Velkinburgh JC, Farmer AD, Lewis S, Beavis WD, Schilkey FD, Virk SM, Black CF, Myers MK, Mader LC, Langley RJ, Utsey JP, Kim RW, Roberts RC, Khalsa SK, Garcia M, Ambriz-Griffith V, Harlan R, Czika W, Martin S, Wolfinger RD, Perrone-Bizzozero NI, Schroth GP and Kingsmore SF: Genomic convergence analysis of schizophrenia: mRNA sequencing reveals altered synaptic vesicular transport in post-mortem cerebellum. PLoS One 3: e3625, 2008.
16. Fitch WM: On the problem of discovering the most parsimonious tree. Amer Natur 111: 223, 1977.
17. Miller NA, Kingsmore SF, Farmer AD, Langley RJ and Mudge J: Management of high-throughput DNA sequencing projects: Alpheus. J Comp Sci Syst Biol 1: 132, 2008.
18. Edwards AWF and Cavalli-Sforza LL: The reconstruction of evolution. Ann Hum Genet 27: 104, 1963.
19. EcK RV and Dayhoff MO: Atlas of Protein Sequence and Structure. Biomedical Research Foundation, Silver Spring, MD, 1966.
20. Merlo LM, Pepper JW, Reid BJ and Maley CC: Cancer as an evolutionary and ecological process. Nat Rev Cancer 6: 924-935, 2006.
21. Shibata D: Molecular tumor clocks and dynamic phenotype. Am J Pathol 151: 643-646, 1997.
22. Shibata D and Tavare S: Counting divisions in a human somatic cell tree: how, what and why? Cell Cycle 5: 610-614, 2006.