A phylogenetic model for understanding the effect of gene duplication on cancer progression

Nucleic Acids Research

Volumn 42, Issue 5, 2014, Pages 2870-2878

  Ma, Qin ^a   Reeves, Jaxk H ^b   Liberles, David A ^c   Yu, Lili ^d   Chang, Zheng ^e   Zhao, Jing ^b   Cui, Juan ^f   Xu, Ying ^a,g,h   Liu, Liang ^a,b  

^a University of Georgia ^*  (United States)

^b UNIVERSITY OF GEORGIA   (United States)

^c UNIVERSITY OF WYOMING   (United States)

^d GEORGIA SOUTHERN UNIVERSITY   (United States)

^e SHANDONG UNIVERSITY   (China)

^f UNIVERSITY OF NEBRASKA LINCOLN   (United States)

^g BioEnergy Science Center   (United States)

^h JILIN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANCER GROWTH; CANCER INCIDENCE; CANCER STAGING; CDH4 GENE; CLPS GENE; CLSTN2 GENE; CONTROLLED STUDY; EML5 GENE; GENE; GENE DELETION; GENE DUPLICATION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC MODEL; HUMAN; HUMAN TISSUE; NPEPL1 GENE; PHYLOGENETIC MODEL; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; SENP5 GENE; SPTB GENE; STOMACH CANCER; VAMP7 GENE; XAGE 4 GENE;

DISEASE PROGRESSION; GENE DELETION; GENE DUPLICATION; GENES, DUPLICATE; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MODELS, STATISTICAL; PHYLOGENY; STOMACH NEOPLASMS;

EID: 84898935755     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1320     Document Type: Article

References (51)

1. Siegel, R., Ward, E., Brawley, O. and Jemal, A. (2011) Cancer statistics. A Cancer J. Clinicians, 61, 212-236.
2. Brosnan, J.A. and Iacobuzio-Donahue, C.A. (2012) A new branch on the tree: Next-generation sequencing in the study of cancer evolution. Semin. Cell Dev. Biol., 23, 237-242.
3. Iacobuzio-Donahue, C.A. (2012) Genetic evolution of pancreatic cancer: Lessons learnt from the pancreatic cancer genome sequencing project. Gut, 61, 1085-1094.
4. Ma, Q.C., Ennis, C.A. and Aparicio, S. (2012) Opening Pandora's Box-The new biology of driver mutations and clonal evolution in cancer as revealed by next generation sequencing. Curr. Opin. Genet. Dev., 22, 3-9.
5. Jones, S., Chen, W.-d., Parmigiani, G., Diehl, F., Beerenwinkel, N., Antal, T., Traulsen, A., Nowak, M.A., Siegel, C., Velculescu, V.E. et al. (2008) Comparative lesion sequencing provides insights into tumor evolution. Proc. Natl Acad. Sci. USA, 105, 4283-4288.
6. Prisman, E.Z., Gafni, A. and Finelli, A. (2011) Testing the evolution process of prostate-specific antigen in early stage prostate cancer: What is the proper underlying model? Stat. Med., 30, 3038-3049.
7. Ayala, F.J. (1977) 'Nothing in biology makes sense except in the light of evolution': Theodosius Dobzhansky: 1900-1975. J. Hered., 68, 3-10.
8. Greaves, M. and Maley, C.C. (2012) Clonal evolution in cancer. Nature, 481, 306-313.
9. Erren, T.C. (2009) On the origin of cancer: Evolution and a mutation paradox. Med. Hypotheses, 73, 124-125.
10. Aktipis, C.A., Kwan, V.S.Y., Johnson, K.A., Neuberg, S.L. and Maley, C.C. (2011) Overlooking evolution: A systematic analysis of cancer relapse and therapeutic resistance research. Plos One, 6.
11. Calcagno, A.M. (2011) Evolution of drug resistance in cancer: The emergence of unique mechanisms and novel techniques. Mol. Pharmaceutics, 8, 1993-1993.
12. Gillies, R.J., Verduzco, D. and Gatenby, R.A. (2012) Evolutionary dynamics of carcinogenesis and why targeted therapy does not work. Nat. Rev. Cancer, 12, 487-493.
13. Goymer, P. (2008) Natural selection: The evolution of cancer. Nature, 454, 1046-1048.
14. Allred, D.C., Wu, Y., Mao, S., Nagtegaal, I.D., Lee, S., Perou, C.M., Mohsin, S.K., O'Connell, P., Tsimelzon, A. and Medina, D. (2008) Ductal carcinoma in situ and the emergence of diversity during breast cancer evolution. Clin. Cancer Res., 14, 370-378.
15. Ewald, P.W. and Ewald, H.A.S. (2012) Infection, mutation, and cancer evolution. J. Mol. Med., 90, 535-541.
16. Gerlinger, M., Rowan, A.J., Horswell, S., Larkin, J., Endesfelder, D., Gronroos, E., Martinez, P., Matthews, N., Stewart, A., Tarpey, P. et al. (2012) Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N. Engl. J. Med., 366, 883-892.
17. Greaves, M. (2000) Cancer: The Evolutionary Legacy. Oxford University Press, Oxford.
18. Yu, K.-D. and Shao, Z.-M. (2012) Initiation, evolution, phenotype and outcome of BRCA1 and BRCA2 mutation-Associated breast cancer. Nat. Rev. Cancer, 12, 372-373.
19. Muto, T., Bussey, H.J. and Morson, B.C. (1975) The evolution of cancer of the colon and rectum. Cancer, 36, 2251-2270.
20. Merlo, L.M.F., Pepper, J.W., Reid, B.J. and Maley, C.C. (2006) Cancer as an evolutionary and ecological process. Nat. Rev. Cancer, 6, 924-935.
21. Otsuka, J. (2011) The large-scale evolution by generating new genes from gene duplication; similarity and difference between monoploid and diploid organisms. J. Theor. Biol., 278, 120-126.
22. Podlaha, O., Riester, M., De, S. and Michor, F. (2012) Evolution of the cancer genome. Trends Genet., 28, 155-163.
23. Nowell, P.C. (1976) The clonal evolution of tumor cell populations. Science, 194, 23-28.
24. Gillies, R.J., Verduzco, D. and Gatenby, R.A. (2012) Evolutionary dynamics of carcinogenesis and why targeted therapy does not work. Nat. Rev. Cancer, 12, 487-493.
25. Wu, X., Northcott, P.A., Dubuc, A., Dupuy, A.J., Shih, D.J.H., Witt, H., Croul, S., Bouffet, E., Fults, D.W., Eberhart, C.G. et al. (2012) Clonal selection drives genetic divergence of metastatic medulloblastoma. Nature, 482, 529-533.
26. Clifford, S.C. (2012) Cancer genetics: Evolution after tumour spread. Nature, 482, 481-482.
27. Hou, Y., Song, L., Zhu, P., Zhang, B., Tao, Y., Xu, X., Li, F., Wu, K., Liang, J., Shao, D. et al. (2012) Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell, 148, 873-885.
28. Xu, X., Hou, Y., Yin, X., Bao, L., Tang, A., Song, L., Li, F., Tsang, S., Wu, K., Wu, H. et al. (2012) Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell, 148, 886-895.
29. Caldas, C. (2012) Cancer sequencing unravels clonal evolution. Nat. Biotechnol., 30, 408-410.
30. Thomas, R.K., Nickerson, E., Simons, J.F., Janne, P.A., Tengs, T., Yuza, Y., Garraway, L.A., LaFramboise, T., Lee, J.C., Shah, K. et al. (2006) Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing. Nat. Med., 12, 852-855.
31. Ciullo, M., Debily, M.A., Rozier, L., Autiero, M., Billault, A., Mayau, V., El Marhomy, S., Guardiola, J., Bernheim, A., Coullin, P. et al. (2002) Initiation of the breakage-fusion-bridge mechanism through common fragile site activation in human breast cancer cells: The model of PIP gene duplication from a break at FRA7I. Hum. Mol. Genet., 11, 2887-2894.
32. Waris, G. and Ahsan, H. (2006) Reactive oxygen species: Role in the development of cancer and various chronic conditions. J. Carcinog., 5, 14.
33. Moelans, C.B., de Weger, R.A., Monsuur, H.N., Vijzelaar, R. and van Diest, P.J. (2010) Molecular profiling of invasive breast cancer by multiplex ligation-dependent probe amplification-based copy number analysis of tumor suppressor and oncogenes. Mod. Pathol., 23, 1029-1039.
34. Cui, J., Yin, Y., Ma, Q., Wang, G., Olman, V., Zhang, Y., Chou, W.-C., Hong, C.S., Zhang, C., Cao, S. et al. (2013) Towards Understanding the Genomic Alterations in Human Gastric Cancer. PLoS Genet., under review.
35. Kim, J.Y., Shin, N.R., Kim, A., Lee, H.J., Park, W.Y., Lee, C.H., Huh, G.Y. and Park do, Y. (2013) Microsatellite instability status in gastric cancer: A reappraisal of its clinical significance and relationship with mucin phenotypes. Korean J. Pathol., 47, 28-35.
36. Ottini, L., Falchetti, M., Lupi, R., Rizzolo, P., Agnese, V., Colucci, G., Bazan, V. and Russo, A. (2006) Patterns of genomic instability in gastric cancer: Clinical implications and perspectives. Ann. Oncol., 17(Suppl 7), vii97-vii102.
37. Pennisi, E. (2012) Genomics. ENCODE project writes eulogy for junk DNA. Science, 337, 1159-1161.
38. Hahn, M.W., De Bie, T., Stajich, J.E., Nguyen, C. and Cristianini, N. (2005) Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res., 15, 1153-1160. (Pubitemid 41126871
39. Liu, L., Yu, L., Kalavacharla, V. and Liu, Z. (2011) A Bayesian model for gene family evolution. BMC Bioinformatics, 12, 426.
40. Felsenstein, J. (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol., 17, 368-376.
41. Byrd, R.H., Lu, P.H., Nocedal, J. and Zhu, C.Y. (1995) A limited memory algorithm for bound constrained optimization. Siam. J. Sci. Comput., 16, 1190-1208.
42. Huang, D.W., Sherman, B.T. and Lempicki, R.A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc., 4, 44-57.
43. McKee, M.L. and Kerwin, S.M. (2008) Synthesis, metal ion binding, and biological evaluation of new anticancer 2-(20-hydroxyphenyl)benzoxazole analogs of UK-1. Bioorganic Med. Chem., 16, 1775-1783.
44. Kampen, K.R. (2011) Membrane proteins: The key players of a cancer cell. J. Membrane Biol., 242, 69-74.
45. Zaman, G.J., Versantvoort, C.H., Smit, J.J., Eijdems, E.W., de Haas, M., Smith, A.J., Broxterman, H.J., Mulder, N.H., de Vries, E.G., Baas, F. et al. (1993) Analysis of the expression of MRP, the gene for a new putative transmembrane drug transporter, in human multidrug resistant lung cancer cell lines. Cancer Res., 53, 1747-1750. (Pubitemid 23127097
46. Klein, R.J., Zeiss, C., Chew, E.Y., Tsai, J.Y., Sackler, R.S., Haynes, C., Henning, A.K., SanGiovanni, J.P., Mane, S.M., Mayne, S.T. et al. (2005) Complement factor H polymorphism in age-related macular degeneration. Science, 308, 385-389. (Pubitemid 40530070
47. Lawrence, M.S., Stojanov, P., Polak, P., Kryukov, G.V., Cibulskis, K., Sivachenko, A., Carter, S.L., Stewart, C., Mermel, C.H., Roberts, S.A. et al. (2013) Mutational heterogeneity in cancer and the search for new cancer-Associated genes. Nature, 499, 214-218.
48. Johnson, A.D. and O'Donnell, C.J. (2009) An open access database of genome-wide association results. BMC Med. Genet., 10, 6.
49. Desmedt, C., Haibe-Kains, B., Wirapati, P., Buyse, M., Larsimont, D., Bontempi, G., Delorenzi, M., Piccart, M. and Sotiriou, C. (2008) Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes. Clin. Cancer Res., 14, 5158-5165.
50. Konrad, A., Teufel, A.I., Grahnen, J.A. and Liberles, D.A. (2011) Toward a general model for the evolutionary dynamics of gene duplicates. Genome Biol. Evol., 3, 1197-1209.
51. Slatkin, M. and Pollack, J.L. (2006) The concordance of gene trees and species trees at two linked loci. Genetics, 172, 1979-1984.