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Comprehensive identification of mutational cancer driver genes across 12 tumor types
Open accessAbstract
With the ability to fully sequence tumor genomes/exomes, the quest for cancer driver genes can now be undertaken in an unbiased manner. However, obtaining a complete catalog of cancer genes is difficult due to the heterogeneous molecular nature of the disease and the limitations of available computational methods. Here we show that the combination of complementary methods allows identifying a comprehensive and reliable list of cancer driver genes. We provide a list of 291 high-confidence cancer driver genes acting on 3,205 tumors from 12 different cancer types. Among those genes, some have not been previously identified as cancer drivers and 16 have clear preference to sustain mutations in one specific tumor type. The novel driver candidates complement our current picture of the emergence of these diseases. In summary, the catalog of driver genes and the methodology presented here open new avenues to better understand the mechanisms of tumorigenesis.
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Cites
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
A method and server for predicting damaging missense mutations.
Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., Bork, P., Kondrashov, A. S., & Sunyaev, S. R. (2010) · Nature Methods · doi:10.1038/nmeth0410-248 · Cited by 13,194
The cancer genome atlas pan-cancer analysis project
The Cancer Genome Atlas Research Network, Weinstein, J. N., Collisson, E. A., Mills, G. B., Shaw, K. R. M., Ozenberger, B. A., Ellrott, K., Shmulevich, I., Sander, C., & Stuart, J. M. (2013) · Nature Genetics · doi:10.1038/ng.2764 · Cited by 9,092
Vogelstein, B., Papadopoulos, N., Velculescu, V. E., Zhou, S., Diaz, L. A., & Kinzler, K. W. (2013) · Science · doi:10.1126/science.1235122 · Cited by 7,863
Comprehensive genomic characterization defines human glioblastoma genes and core pathways
The Cancer Genome Atlas Research Network (2008) · Nature · doi:10.1038/nature07385 · Cited by 7,735
SIFT: predicting amino acid changes that affect protein function
Ng, P. C. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg509 · Cited by 6,577
Mutational heterogeneity in cancer and the search for new cancer-associated genes
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) · Nature · doi:10.1038/nature12213 · Cited by 5,461
Self-citationMermel, C. H., Schumacher, S. E., Hill, B., Meyerson, M. L., Beroukhim, R., & Getz, G. (2011) · Genome Biology · doi:10.1186/gb-2011-12-4-r41 · Cited by 3,550
Self-citationStratton, M. R., Campbell, P. J., & Futreal, P. A. (2009) · Nature · doi:10.1038/nature07943 · Cited by 3,449
A census of human cancer genes
Futreal, P. A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N., & Stratton, M. R. (2004) · Nature Reviews Cancer · doi:10.1038/nrc1299 · Cited by 3,184
Patterns of somatic mutation in human cancer genomes
Greenman, C., Stephens, P., Smith, R., Dalgliesh, G. L., Hunter, C., Bignell, G., Davies, H., Teague, J., Butler, A., Stevens, C., et al. (2007) · Nature · doi:10.1038/nature05610 · Cited by 3,080
A landscape of driver mutations in melanoma
Hodis, E., Watson, I. R., Kryukov, G. V., Arold, S. T., Imielinski, M., Theurillat, J.-P., Nickerson, E., Auclair, D., Li, L., Place, C., et al. (2012) · Cell · doi:10.1016/j.cell.2012.06.024 · Cited by 2,610
Self-citationKEGG for representation and analysis of molecular networks involving diseases and drugs
Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., & Hirakawa, M. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp896 · Cited by 2,322
International network of cancer genome projects
The International Cancer Genome Consortium (2010) · Nature · doi:10.1038/nature08987 · Cited by 2,299
Predicting the functional impact of protein mutations: application to cancer genomics
Reva, B., Antipin, Y., & Sander, C. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr407 · Cited by 2,002
Mechanism of activation of a human oncogene
Tabin, C. J., Bradley, S. M., Bargmann, C. I., Weinberg, R. A., Papageorge, A. G., Scolnick, E. M., Dhar, R., Lowy, D. R., & Chang, E. H. (1982) · Nature · doi:10.1038/300143a0 · Cited by 1,393
Reddy, E. P., Reynolds, R. K., Santos, E., & Barbacid, M. (1982) · Nature · doi:10.1038/300149a0 · Cited by 1,391
Lessons from the Cancer Genome
Garraway, L. A., & Lander, E. S. (2013) · Cell · doi:10.1016/j.cell.2013.03.002 · Cited by 1,308
Pathway Commons, a web resource for biological pathway data
Cerami, E. G., Gross, B. E., Demir, E., Rodchenkov, I., Babur, O., Anwar, N., Schultz, N., Bader, G. D., & Sander, C. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1039 · Cited by 1,101
Self-citationA human functional protein interaction network and its application to cancer data analysis
Wu, G., Feng, X., & Stein, L. (2010) · Genome Biology · doi:10.1186/gb-2010-11-5-r53 · Cited by 692
MuSiC: Identifying mutational significance in cancer genomes
Dees, N. D., Zhang, Q., Kandoth, C., Wendl, M. C., Schierding, W., Koboldt, D. C., Mooney, T. B., Callaway, M. B., Dooling, D., Mardis, E. R., et al. (2012) · Genome Research · doi:10.1101/gr.134635.111 · Cited by 677
Self-citationIntOGen-mutations identifies cancer drivers across tumor types
Gonzalez-Perez, A., Perez-Llamas, C., Deu-Pons, J., Tamborero, D., Schroeder, M. P., Jene-Sanz, A., Santos, A., & Lopez-Bigas, N. (2013) · Nature Methods · doi:10.1038/nmeth.2642 · Cited by 586
Self-citationPTEN-deficient cancers depend on PIK3CB
Wee, S., Wiederschain, D., Maira, S.-M., Loo, A., Miller, C., deBeaumont, R., Stegmeier, F., Yao, Y.-M., & Lengauer, C. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0802655105 · Cited by 545
OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes
Tamborero, D., Gonzalez-Perez, A., & Lopez-Bigas, N. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt395 · Cited by 490
Self-citationFunctional impact bias reveals cancer drivers
Gonzalez-Perez, A., & Lopez-Bigas, N. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks743 · Cited by 332
Self-citationSystematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers
Reimand, J., & Bader, G. D. (2013) · Molecular Systems Biology · doi:10.1038/msb.2012.68 · Cited by 275
Self-citationGitools: Analysis and Visualisation of Genomic Data Using Interactive Heat-Maps
Perez-Llamas, C., & Lopez-Bigas, N. (2011) · PLoS ONE · doi:10.1371/journal.pone.0019541 · Cited by 265
Self-citationFOXA1: a transcription factor with parallel functions in development and cancer
Bernardo, G. M., & Keri, R. A. (2012) · Bioscience Reports · doi:10.1042/bsr20110046 · Cited by 225
Computational approaches to identify functional genetic variants in cancer genomes
the International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group (2013) · Nature Methods · doi:10.1038/nmeth.2562 · Cited by 171
The mutational landscape of phosphorylation signaling in cancer
Reimand, J., Wagih, O., & Bader, G. D. (2013) · Scientific Reports · doi:10.1038/srep02651 · Cited by 162
Self-citationTGFβ-induced downregulation of E-cadherin-based cell-cell adhesion depends on PI3-kinase and PTEN
Vogelmann, R., Nguyen-tat, M.-D., Giehl, K., Adler, G., Wedlich, D., & Menke, A. (2005) · Journal of Cell Science · doi:10.1242/jcs.02594 · Cited by 159
DNA damage in stem cells activates p21, inhibits p53, and induces symmetric self-renewing divisions.
Insinga, A., Cicalese, A., Faretta, M., Gallo, B., Albano, L., Ronzoni, S., Furia, L., Viale, A., & Pelicci, P. G. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1213394110 · Cited by 140
Expression and role of Foxa proteins in prostate cancer
Mirosevich, J., Gao, N., Gupta, A., Shappell, S. B., Jove, R., & Matusik, R. J. (2005) · The Prostate · doi:10.1002/pros.20299 · Cited by 132
Recruitment of the Cell Cycle Checkpoint Kinase ATR to Chromatin during S-phase
Dart, D. A., Adams, K. E., Akerman, I., & Lakin, N. D. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m314212200 · Cited by 124
The function of p27 KIP1 during tumor development
Lee, J., & Kim, S. S. (2009) · Experimental & Molecular Medicine · doi:10.3858/emm.2009.41.11.102 · Cited by 112
Colorectal carcinomas in mice lacking the catalytic subunit of PI(3)Kγ
Sasaki, T., Irie-Sasaki, J., Horie, Y., Bachmaier, K., Fata, J. E., Li, M., Suzuki, A., Bouchard, D., Ho, A., Redston, M. S., et al. (2000) · Nature · doi:10.1038/35022585 · Cited by 100
IKKα Activation of NOTCH Links Tumorigenesis via FOXA2 Suppression
Liu, M., Lee, D., Chen, C., Yen, C.-J., Li, L., Lee, H.-J., Chang, C.-J., Chang, W., Hsu, J.-M., Kuo, H.-P., et al. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.11.018 · Cited by 95
Nuclear but Not Cytosolic Phosphoinositide 3-Kinase Beta Has an Essential Function in Cell Survival
Kumar, A., Redondo-Muñóz, J., Pérez-García, V., Cortés, I., Chagoyen, M., & Carrera, A. C. (2011) · Molecular and Cellular Biology · doi:10.1128/mcb.01313-10 · Cited by 85
Williamson, E. A., Wolf, I., O’Kelly, J., Bose, S., Tanosaki, S., & Koeffler, H. P. (2005) · Oncogene · doi:10.1038/sj.onc.1209170 · Cited by 79
Rausa, F. M., Tan, Y., & Costa, R. H. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.23.2.437-449.2003 · Cited by 77
Semba, S., Itoh, N., Ito, M., et al. (2002) · PubMed · Cited by 75
Imamura, Y., Sakamoto, S., Endo, T., Utsumi, T., Fuse, M., Suyama, T., Kawamura, K., Imamoto, T., Yano, K., Uzawa, K., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042456 · Cited by 61
Marqués, M., Kumar, A., Cortés, I., Gonzalez-García, A., Hernández, C., Moreno-Ortiz, M. C., & Carrera, A. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.01786-07 · Cited by 61
Oncogenic transformation and experimental models of human cancer
Anna, C. S. (2007) · Frontiers in bioscience · doi:10.2741/2661 · Cited by 56
Hill, K. M., Kalifa, S., Das, J., Bhatti, T., Gay, M. D., Williams, D., Taliferro-Smith, L., & Marzo, A. D. D. (2010) · The Prostate · doi:10.1002/pros.21108 · Cited by 47
Tamborero, D., López-Bigas, N., & González-Pérez, A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0055489 · Cited by 34
Self-citationOpposite roles of FOXA1 and NKX2‐1 in lung cancer progression
Deutsch, L. S., Wrage, M., Koops, S., Glatzel, M., Uzunoglu, F. G., Kutup, A., Hinsch, A., Sauter, G., Izbicki, J. R., Pantel, K., et al. (2012) · Genes Chromosomes and Cancer · doi:10.1002/gcc.21950 · Cited by 29
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Tissue-based map of the human proteome
Uhlén, M., Fagerberg, L., Hallström, B. M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, Å., Kampf, C., Sjöstedt, E., Asplund, A., et al. (2015) · Science · doi:10.1126/science.1260419 · Cited by 15,286
The cancer genome atlas pan-cancer analysis project
The Cancer Genome Atlas Research Network, Weinstein, J. N., Collisson, E. A., Mills, G. B., Shaw, K. R. M., Ozenberger, B. A., Ellrott, K., Shmulevich, I., Sander, C., & Stuart, J. M. (2013) · Nature Genetics · doi:10.1038/ng.2764 · Cited by 9,092
The consensus molecular subtypes of colorectal cancer
Guinney, J., Dienstmann, R., Wang, X., de Reyniès, A., Schlicker, A., Soneson, C., Marisa, L., Roepman, P., Nyamundanda, G., Angelino, P., et al. (2015) · Nature Medicine · doi:10.1038/nm.3967 · Cited by 5,170
Discovery and saturation analysis of cancer genes across 21 tumour types
Lawrence, M. S., Stojanov, P., Mermel, C. H., Robinson, J. T., Garraway, L. A., Golub, T. R., Meyerson, M., Gabriel, S. B., Lander, E. S., & Getz, G. (2014) · Nature · doi:10.1038/nature12912 · Cited by 3,096
Self-citationA Landscape of Pharmacogenomic Interactions in Cancer
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Self-citation
Metadata
- Authors
- Tamborero, D., Gonzalez-Perez, A., Perez-Llamas, C., Deu-Pons, J., Kandoth, C., Reimand, J., Lawrence, M. S., Getz, G., Bader, G. D., Ding, L., & Lopez-Bigas, N.
- Venue
- Scientific Reports
- Published
- 2013-10-02
- Volume
- 3
- Issue
- 1
- Pages
- 2650-2650
- ISSN
- 2045-2322 (ISSN-L)
- OpenAlex
- W2096460732
- Cited by
- 484
- References
- 47
- FWCI
- 17.69
- Type
- journal article
- Language
- en
- Open access
- gold
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