Aplicação de simulated annealing para descobrir mutações drivers
Abstract
Cells with driver mutations can proliferate faster than other cells, generating more daughter cells and causing the appearance of the tumor. In this context, there are computational methods for identifying possible driver mutations in a sample of cells. DriverNet is a method for classifying mutations in a sample, indicating those most likely to be driver mutations. This work presents a new proposal to identify driver mutations based on the DriverNet method. The new proposal, which requires a smaller set of input data than the DriverNet method, identified genes related to cancer from datasets from the TCGA project.
References
Cheng, F., Zhao, J., and Zhao, Z. (2016). Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. Briefings in bioinformatics, 17 4:642-56.
Croft, D., Mundo, A. F., Haw, R., Milacic, M.,Weiser, J.,Wu, G., Caudy, M., Garapati, P., Gillespie, M., Kamdar, M. R., Jassal, B., Jupe, S., Matthews, L., May, B., Palatnik, S., Rothfels, K., Shamovsky, V., Song, H., Williams, M., Birney, E., Hermjakob, H., Stein, L., and D'Eustachio, P. (2014). The reactome pathway knowledgebase. Nucleic acids research, 42(D1):D472-D477.
Cutigi, J. F., Evangelista, A. F., and Simão, A. d. S. (2020). Approaches for the identification of driver mutations in cancer: a tutorial from a computational perspective. Journal of Bioinformatics and Computational Biology, 18(3):2050016:1-2050016:32.
Dimitrakopoulos, C. and Beerenwinkel, N. (2016). Computational approaches for the identification of cancer genes and pathways. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 9.
Greenman, C., Stephens, P., Smith, R., Dalgliesh, G., Hunter, C., Bignell, G., Davies, H., Teague, J., Butler, A., Stevens, C., Edkins, S., O'Meara, S., Vastrik, I., Schmidt, E., Avis, T., Barthorpe, S., Bhamra, G., Buck, G., Choudhury, B., and Stratton, M. (2007). Patterns of somatic mutation in human cancer genomes. Nature, 446:153-8.
Haber, D. and Settleman, J. (2007). Cancer: Drivers and passengers. Nature, 446:145-6.
Hou, J. and Ma, J. (2013). Identifying Driver Mutations in Cancer, volume 4, pages 33-56. Genome Medicine.
Kirkpatrick, S., Gelatt, C. D., and Vecchi, M. P. (1983). Optimization by simulated annealing. Science, 220(4598):671-680.
Lever, J., Zhao, E. Y., Grewal, J., Jones, M. R., and Jones, S. J. M. (2019). Cancermine: a literature-mined resource for drivers, oncogenes and tumor suppressors in cancer. Nature Methods, 16(6):505-507.
Li, H. T., Zhang, Y. L., Zheng, C. H., and Wang, H. Q. (2014). Simulated annealing based algorithm for identifying mutated driver pathways in cancer. BioMed Research International, 2014.
Moreira, L. M. (2015). Ciências genômicas: fundamentos e aplicações. Sociedade Brasileira de Genética.
Pham, V., Liu, L., Bracken, C., Goodall, G., Li, J., and le, T. (2021). Computational methods for cancer driver discovery: A survey. Theranostics, 11:5553-5568.
Raphael, B. J., Dobson, J., Oesper, L., and Vandin, F. (2014). Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine. Genome Medicine, 6:5 - 5.
TCGA data portal (2018). The Cancer Genome Atlas Program.
Vandin, F., Upfal, E., and Raphael, B. J. (2012). De novo discovery of mutated driver pathways in cancer. Genome research, 22(2):375-385.
Yang, L., Chen, R., Goodison, S., and Sun, Y. (2021). An efficient and effective method to identify significantly perturbed subnetworks in cancer. Nature Computational Science, 1:79-88.
Cerny, V. (1985). Thermodynamical approach to the traveling salesman problem: An efficient simulation algorithm. Journal of Optimization Theory and Applications, 45:41-51.
