Integrated analysis of recurrent properties of cancer genes to identify novel drivers

被引：26

作者：

D'Antonio, Matteo ^{[1
]}

Ciccarelli, Francesca D. ^{[1
]}

机构：

[1] European Inst Oncol, Dept Expt Oncol, I-20139 Milan, Italy

来源：

GENOME BIOLOGY | 2013年 / 14卷 / 05期

关键词：

Driver mutations; cancer genetic heterogeneity; interaction network; gene duplication; gene origin; gene expression; ACUTE MYELOID-LEUKEMIA; HIGH-THROUGHPUT ANNOTATION; NECROSIS-FACTOR-ALPHA; NF-KAPPA-B; SOMATIC MUTATIONS; FREQUENT MUTATION; CELL-ADHESION; INACTIVATING MUTATIONS; ADAPTER PROTEIN; GENOME;

D O I：

10.1186/gb-2013-14-5-r52

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 [微生物学]; 090105 [作物生产系统与生态工程];

摘要：

The heterogeneity of cancer genomes in terms of acquired mutations complicates the identification of genes whose modification may exert a driver role in tumorigenesis. In this study, we present a novel method that integrates expression profiles, mutation effects, and systemic properties of mutated genes to identify novel cancer drivers. We applied our method to ovarian cancer samples and were able to identify putative drivers in the majority of carcinomas without mutations in known cancer genes, thus suggesting that it can be used as a complementary approach to find rare driver mutations that cannot be detected using frequency-based approaches.

引用

页数：17

共 141 条

[1]

Expressions of Rac1, Tiam1 and Cdc42 in retinoblastoma [J].

Adithi, Mohan ;

Venkatesan, Nahini ;

Kandalam, Mallikarjuna ;

Biswas, Jyotirmay ;

Krishnakumar, Subramanian .

EXPERIMENTAL EYE RESEARCH, 2006, 83 (06) :1446-1452

[2]

A method and server for predicting damaging missense mutations [J].

Adzhubei, Ivan A. ;

Schmidt, Steffen ;

Peshkin, Leonid ;

Ramensky, Vasily E. ;

Gerasimova, Anna ;

Bork, Peer ;

Kondrashov, Alexey S. ;

Sunyaev, Shamil R. .

NATURE METHODS, 2010, 7 (04) :248-249

[3]

Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1 [J].

Agrawal, Nishant ;

Frederick, Mitchell J. ;

Pickering, Curtis R. ;

Bettegowda, Chetan ;

Chang, Kyle ;

Li, Ryan J. ;

Fakhry, Carole ;

Xie, Tong-Xin ;

Zhang, Jiexin ;

Wang, Jing ;

Zhang, Nianxiang ;

El-Naggar, Adel K. ;

Jasser, Samar A. ;

Weinstein, John N. ;

Trevino, Lisa ;

Drummond, Jennifer A. ;

Muzny, Donna M. ;

Wu, Yuanqing ;

Wood, Laura D. ;

Hruban, Ralph H. ;

Westra, William H. ;

Koch, Wayne M. ;

Califano, Joseph A. ;

Gibbs, Richard A. ;

Sidransky, David ;

Vogelstein, Bert ;

Velculescu, Victor E. ;

Papadopoulos, Nickolas ;

Wheeler, David A. ;

Kinzler, Kenneth W. ;

Myers, Jeffrey N. .

SCIENCE, 2011, 333 (6046) :1154-1157

[4]

Gelsolin negatively regulates the activity of tumor suppressor p53 through their physical interaction in hepatocarcinoma HepG2 cells [J].

An, Joo-Hee ;

Kim, Jung-Woong ;

Jang, Sang-Min ;

Kim, Chul-Hong ;

Kang, Eun-Jin ;

Choi, Kyung-Hee .

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2011, 412 (01) :44-49

[5]

The IntAct molecular interaction database in 2010 [J].

Aranda, B. ;

Achuthan, P. ;

Alam-Faruque, Y. ;

Armean, I. ;

Bridge, A. ;

Derow, C. ;

Feuermann, M. ;

Ghanbarian, A. T. ;

Kerrien, S. ;

Khadake, J. ;

Kerssemakers, J. ;

Leroy, C. ;

Menden, M. ;

Michaut, M. ;

Montecchi-Palazzi, L. ;

Neuhauser, S. N. ;

Orchard, S. ;

Perreau, V. ;

Roechert, B. ;

van Eijk, K. ;

Hermjakob, H. .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D525-D531

[6]

Approaches to define antigen receptor-induced serine kinase signal transduction pathways [J].

Astoul, E ;

Laurence, AD ;

Totty, N ;

Beer, S ;

Alexander, DR ;

Cantrell, DA .

JOURNAL OF BIOLOGICAL CHEMISTRY, 2003, 278 (11) :9267-9275

[7]

Evolutionary Theory of Cancer [J].

Attolini, Camille Stephan-Otto ;

Michor, Franziska .

YEAR IN EVOLUTIONARY BIOLOGY 2009, 2009, 1168 :23-51

[8]

Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy [J].

Barretina, Jordi ;

Taylor, Barry S. ;

Banerji, Shantanu ;

Ramos, Alexis H. ;

Lagos-Quintana, Mariana ;

DeCarolis, Penelope L. ;

Shah, Kinjal ;

Socci, Nicholas D. ;

Weir, Barbara A. ;

Ho, Alan ;

Chiang, Derek Y. ;

Reva, Boris ;

Mermel, Craig H. ;

Getz, Gad ;

Antipin, Yevgenyi ;

Beroukhim, Rameen ;

Major, John E. ;

Hatton, Charles ;

Nicoletti, Richard ;

Hanna, Megan ;

Sharpe, Ted ;

Fennell, Tim J. ;

Cibulskis, Kristian ;

Onofrio, Robert C. ;

Saito, Tsuyoshi ;

Shukla, Neerav ;

Lau, Christopher ;

Nelander, Sven ;

Silver, Serena J. ;

Sougnez, Carrie ;

Viale, Agnes ;

Winckler, Wendy ;

Maki, Robert G. ;

Garraway, Levi A. ;

Lash, Alex ;

Greulich, Heidi ;

Root, David E. ;

Sellers, William R. ;

Schwartz, Gary K. ;

Antonescu, Cristina R. ;

Lander, Eric S. ;

Varmus, Harold E. ;

Ladanyi, Marc ;

Sander, Chris ;

Meyerson, Matthew ;

Singer, Samuel .

NATURE GENETICS, 2010, 42 (08) :715-U103

[9]

NCBI GEO: archive for functional genomics data sets-10 years on [J].

Barrett, Tanya ;

Troup, Dennis B. ;

Wilhite, Stephen E. ;

Ledoux, Pierre ;

Evangelista, Carlos ;

Kim, Irene F. ;

Tomashevsky, Maxim ;

Marshall, Kimberly A. ;

Phillippy, Katherine H. ;

Sherman, Patti M. ;

Muertter, Rolf N. ;

Holko, Michelle ;

Ayanbule, Oluwabukunmi ;

Yefanov, Andrey ;

Soboleva, Alexandra .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D1005-D1010

[10]

Integrated genomic analyses of ovarian carcinoma [J].

Bell, D. ;

Berchuck, A. ;

Birrer, M. ;

Chien, J. ;

Cramer, D. W. ;

Dao, F. ;

Dhir, R. ;

DiSaia, P. ;

Gabra, H. ;

Glenn, P. ;

Godwin, A. K. ;

Gross, J. ;

Hartmann, L. ;

Huang, M. ;

Huntsman, D. G. ;

Iacocca, M. ;

Imielinski, M. ;

Kalloger, S. ;

Karlan, B. Y. ;

Levine, D. A. ;

Mills, G. B. ;

Morrison, C. ;

Mutch, D. ;

Olvera, N. ;

Orsulic, S. ;

Park, K. ;

Petrelli, N. ;

Rabeno, B. ;

Rader, J. S. ;

Sikic, B. I. ;

Smith-McCune, K. ;

Sood, A. K. ;

Bowtell, D. ;

Penny, R. ;

Testa, J. R. ;

Chang, K. ;

Dinh, H. H. ;

Drummond, J. A. ;

Fowler, G. ;

Gunaratne, P. ;

Hawes, A. C. ;

Kovar, C. L. ;

Lewis, L. R. ;

Morgan, M. B. ;

Newsham, I. F. ;

Santibanez, J. ;

Reid, J. G. ;

Trevino, L. R. ;

Wu, Y. -Q. ;

Wang, M. .

NATURE, 2011, 474 (7353) :609-615

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