Inferring the paths of somatic evolution in cancer

Bioinformatics

Volumn 30, Issue 17, 2014, Pages 2456-2463

  Misra, Navodit ^a   Szczurek, Ewa ^a,b   Vingron, Martin ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BAYES THEOREM; CLONAL EVOLUTION; GENETICS; GENOTYPE; HUMAN; MUTATION; NEOPLASM; TUMOR GENE;

ALGORITHMS; BAYES THEOREM; CLONAL EVOLUTION; GENES, NEOPLASM; GENOTYPE; HUMANS; MUTATION; NEOPLASMS;

EID: 84907029453     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu319     Document Type: Article

References (40)

1. Attolini, C.S. et al. (2010) A mathematical framework to determine the temporal sequence of somatic genetic events in cancer. Proc. Natl Acad. Sci. USA, 107, 17604-17609.
2. Balakrishnan, A. et al. (2007) Novel Somatic and germline mutations in cancer candidate genes in glioblastoma, melanoma, and pancreatic carcinoma. Cancer Res., 67, 3545.
3. Bamford, S. et al. (2004) The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br. J. Cancer, 91, 355358.
4. Bissell, M.J. and Hines, W.J. (2011) Why dont we get more cancer? A proposed role of the microenvironment in restraining cancer progression. Nat. Med., 17, 320-329.
5. Bozic, I. et al. (2010) Accumulation of driver and passenger mutations during tumor progression. Proc. Natl Acad. Sci. USA, 107, 18545-18550.
6. Breen, M.S. et al. (2012) Epistasis as the primary factor in molecular evolution. Nature, 490, 535538.
7. Bulashevska, S. et al. (2004) Pathways of urothelial cancer progression suggested by Bayesian network analysis of allelotyping data. Int. J. Cancer, 110, 850-856.
8. Ciriello, G. et al. (2013) Emerging landscape of oncogenic signatures across human cancers. Nat. Genet., 45, 1127-1133.
9. Desper, R. et al. (1999) Inferring tree models for oncogenesis from comparative genome hybridization data. J. Comp. Biol., 6, 37-51.
10. Ding, L. et al. (2008) Somatic mutations affect key pathways in lung adenocarcinoma. Nature, 455, 1069-1075.
11. Fearon, E.R. and Vogelstein, B. (1990) A genetic model for colorectal tumorigenesis. Cell, 61, 759-767.
12. Felsenstein, J. (2004) Inferring Phylogenies. Sinauer Associates, Sunderland, MA.
13. Fisher, R.A. (1918) The correlation between relatives on the supposition of Mendelian inheritance. Trans. R. Soc. Edinb., 52, 399-433.
14. Friedman, N. et al. (1999) Data analysis with bayesian networks: a bootstrap approach. In: Proceedings of the fifteenth conference on Uncertainty in Artificial Intelligence (UAI). pp. 196-205.
15. Friedman, N. et al. (2000) Using Bayesian networks to analyze expression data. J. Comp. Biol., 7, 601-620.
16. Gerstung, M. et al. (2009) Quantifying cancer progression with conjunctive Bayesian networks. Bioinformatics, 25, 2809-2815.
17. Gong, L.I. et al. (2013) Stability-mediated epistasis constrains the evolution of an influenza protein. eLife, 2, e00631.
18. Greenman, C. et al. (2007) Patterns of somatic mutation in human cancer genomes. Nature, 446, 153-158.
19. Hanahan, D. and Weinberg, R.A. (2011) Hallmarks of cancer: the next generation. Cell, 144, 646-674.
20. Hjelm, M. et al. (2006) New probabilistic network models and algorithms for oncogenesis. J. Comp. Biol., 13, 853-865.
21. Kimura, M. (1985) The role of compensatory neutral mutations in molecular evolution. J. Genet., 64, 7-19.
22. Koller, D. and Friedman, N. (2009) Probabilistic Graphical Models: Principles and Techniques. MIT press, Cambridge, MA.
23. Komarova, N.L. et al. (2003) Mutation-selection networks of cancer initiation: tumor suppressor genes and chromosomal instability. J. Theor. Biol., 223, 433-450.
24. Lawrence, M.S. et al. (2013) Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature, 499, 214218.
25. Machado, C. et al. (1998) Human autoantibodies reveal titin as a chromosomal protein. J. Cell Biol., 141, 321-333.
26. Machado, C. and Andrew, D.J. (2000) D-Titin: a giant protein with dual roles in chromosomes and muscles. J. Cell Biol., 151, 639-652.
27. Merlo, L.M.F. et al. (2004) Cancer as an evolutionary and ecological process. Nat. Rev. Cancer, 6, 924-935.
28. Michor, F. et al. (2004) Dynamics of cancer progression. Nat. Rev. Cancer, 4, 197-205.
29. Nik-Zainal, S. et al. (2012) The life history of 21 breast cancers. Cell, 49, 994-1007.
30. Ohgaki, H. et al. (2004) Genetic pathways to glioblastoma: a population-based study. Cancer Res., 64, 6892-6899.
31. Ohgaki, H. and Kleihues, P. (2007) Genetic pathways to primary and secondary glioblastoma. Am. J. Pathol., 170, 1445-1453.
32. Parsons, D.W. et al. (2008) An integrated genomic analysis of glioblastoma multiforme. Science, 321, 1807-1812.
33. Qi, J. et al. (2008) Nuclear localization of the titin Z1Z2Zr domain and role in regulating cell proliferation. Am. J. Cell Physiol., 295, 975-985.
34. Sjöblom, T. et al. (2006) The consensus coding sequences of human breast and colorectal cancers. Science, 314, 268274.
35. Smith, J.M. (1970) Natural selection and the concept of a protein space. Nature, 225, 563-564.
36. Stratton, M.R. et al. (2009) The cancer genome. Nature, 458, 719-724.
37. Teyssier, M. and Koller, D. (2005) Ordering-based search: A simple and effective algorithm for learning Bayesian networks. In: Proceedings of the Fifteenth Conference on Uncertainty in Artificial Intelligence (UAI). pp. 548-549.
38. The Cancer Genome Atlas Research Network. (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455, 1061-1068.
39. The Cancer Genome Atlas Research Network. (2011) Integrated genomic analyses of ovarian carcinoma. Nature, 474, 330-615.
40. Weinreich, D.M. et al. (2005) Perspective: sign epistasis and genetic constraint on evolutionary trajectories. Evolution, 59, 1165-1174.