Deciphering oncogenic drivers: from single genes to integrated pathways

作者: J. Chen , M. Sun , B. Shen

DOI: 10.1093/BIB/BBU039

关键词: Extant taxonCancerComputational biologyCancer mutationsGenomeGeneMutation (genetic algorithm)Function (biology)Biology

摘要: Technological advances in next-generation sequencing have uncovered a wide spectrum of aberrations cancer genomes. The extreme diversity mutations necessitates computational approaches to differentiate between the 'drivers' with vital function progression and those nonfunctional 'passengers'. Although individual driver are routinely identified, mutational profiles different tumors highly heterogeneous. There is growing consensus that pathways rather than single genes primary target mutations. Here we review extant bioinformatics identifying oncogenic drivers at levels, highlighting strategies for discovering networks from mutation data. These will help reduce complexity, thus providing simplified picture cancer.

参考文章(82)
Hege G. Russnes, Nicholas Navin, James Hicks, Anne-Lise Borresen-Dale, Insight into the heterogeneity of breast cancer through next-generation sequencing Journal of Clinical Investigation. ,vol. 121, pp. 3810- 3818 ,(2011) , 10.1172/JCI57088
Uri David Akavia, Oren Litvin, Jessica Kim, Felix Sanchez-Garcia, Dylan Kotliar, Helen C. Causton, Panisa Pochanard, Eyal Mozes, Levi A. Garraway, Dana Pe'er, An Integrated Approach to Uncover Drivers of Cancer Cell. ,vol. 143, pp. 1005- 1017 ,(2010) , 10.1016/J.CELL.2010.11.013
Chris Greenman, Richard Wooster, P. Andrew Futreal, Michael R. Stratton, Douglas F. Easton, Statistical analysis of pathogenicity of somatic mutations in cancer. Genetics. ,vol. 173, pp. 2187- 2198 ,(2006) , 10.1534/GENETICS.105.044677
Joshua S. Kaminker, Yan Zhang, Allison Waugh, Peter M. Haverty, Brock Peters, Dragan Sebisanovic, Jeremy Stinson, William F. Forrest, J. Fernando Bazan, Somasekar Seshagiri, Zemin Zhang, Distinguishing cancer-associated missense mutations from common polymorphisms. Cancer Research. ,vol. 67, pp. 465- 473 ,(2007) , 10.1158/0008-5472.CAN-06-1736
Jüri Reimand, Gary D Bader, Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers Molecular Systems Biology. ,vol. 9, pp. 637- 637 ,(2013) , 10.1038/MSB.2012.68
J. C. Lin, J. Cummins, S. Boca, L. D. Wood, D. W. Parsons, S. Jones, T. Sjoblom, B.-H. Park, R. Parsons, J. Willis, D. Dawson, J. K. V. Willson, T. Nikolskaya, Y. Nikolsky, L. Kopelovich, N. Papadopoulos, L. A. Pennacchio, T.-L. Wang, S. D. Markowitz, G. Parmigiani, K. W. Kinzler, B. Vogelstein, V. E. Velculescu, R. J. Leary, Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers Proceedings of the National Academy of Sciences of the United States of America. ,vol. 105, pp. 16224- 16229 ,(2008) , 10.1073/PNAS.0808041105
Yifei Tang, Wenying Yan, Jiajia Chen, Cheng Luo, Antti Kaipia, Bairong Shen, Identification of novel microRNA regulatory pathways associated with heterogeneous prostate cancer BMC Systems Biology. ,vol. 7, pp. 1- 9 ,(2013) , 10.1186/1752-0509-7-S3-S6
Michael S Lawrence, Petar Stojanov, Paz Polak, Gregory V Kryukov, Kristian Cibulskis, Andrey Sivachenko, Scott L Carter, Chip Stewart, Craig H Mermel, Steven A Roberts, Adam Kiezun, Peter S Hammerman, Aaron McKenna, Yotam Drier, Lihua Zou, Alex H Ramos, Trevor J Pugh, Nicolas Stransky, Elena Helman, Jaegil Kim, Carrie Sougnez, Lauren Ambrogio, Elizabeth Nickerson, Erica Shefler, Maria L Cortés, Daniel Auclair, Gordon Saksena, Douglas Voet, Michael Noble, Daniel DiCara, Pei Lin, Lee Lichtenstein, David I Heiman, Timothy Fennell, Marcin Imielinski, Bryan Hernandez, Eran Hodis, Sylvan Baca, Austin M Dulak, Jens Lohr, Dan-Avi Landau, Catherine J Wu, Jorge Melendez-Zajgla, Alfredo Hidalgo-Miranda, Amnon Koren, Steven A McCarroll, Jaume Mora, Ryan S Lee, Brian Crompton, Robert Onofrio, Melissa Parkin, Wendy Winckler, Kristin Ardlie, Stacey B Gabriel, Charles WM Roberts, Jaclyn A Biegel, Kimberly Stegmaier, Adam J Bass, Levi A Garraway, Matthew Meyerson, Todd R Golub, Dmitry A Gordenin, Shamil Sunyaev, Eric S Lander, Gad Getz, None, Mutational heterogeneity in cancer and the search for new cancer-associated genes Nature. ,vol. 499, pp. 214- 218 ,(2013) , 10.1038/NATURE12213
Lynda Chin, Joe W. Gray, Translating insights from the cancer genome into clinical practice Nature. ,vol. 452, pp. 553- 563 ,(2008) , 10.1038/NATURE06914