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The landscape of somatic copy-number alteration across human cancers
Open accessAbstract
A powerful way to discover key genes with causal roles in oncogenesis is to identify genomic regions that undergo frequent alteration in human cancers. Here we present high-resolution analyses of somatic copy-number alterations (SCNAs) from 3,131 cancer specimens, belonging largely to 26 histological types. We identify 158 regions of focal SCNA that are altered at significant frequency across several cancer types, of which 122 cannot be explained by the presence of a known cancer target gene located within these regions. Several gene families are enriched among these regions of focal SCNA, including the BCL2 family of apoptosis regulators and the NF-kappaBeta pathway. We show that cancer cells containing amplifications surrounding the MCL1 and BCL2L1 anti-apoptotic genes depend on the expression of these genes for survival. Finally, we demonstrate that a large majority of SCNAs identified in individual cancer types are present in several cancer types.
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“More recently, it was found that increased expression of the serine synthesis enzyme phosphoglycerate dehydrogenase (PHGDH) in some cancers can result from copy number gain of a region on chromosome 1p (Beroukhim et al., 2010; Locasale et al., 2011; Possemato et al., 2011) or a consequence of oncogenic signaling, including NRF2 and ATF4 signaling (DeNicola et al., 2015), or hypoxia responses (Sam”
From Targeting Metabolism for Cancer Therapy (2017) · cites this paper as Beroukhim et al., 2010
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“Copy number alterations at 4q21 occur in breast cancer (Beroukhim et al., 2010) and engulf fifteen genes in the amplification peak, including CXCL1-8.”
From A CXCL1 Paracrine Network Links Cancer Chemoresistance and Metastasis (2012) · cites this paper as Beroukhim et al., 2010
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Cites
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482
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
Nowell, P. C. (1976) · Science · doi:10.1126/science.959840 · Cited by 6,471
In Vivo Gene Delivery and Stable Transduction of Nondividing Cells by a Lentiviral Vector
Naldini, L., Blömer, U., Gallay, P., Ory, D., Mulligan, R., Gage, F. H., Verma, I. M., & Trono, D. (1996) · Science · doi:10.1126/science.272.5259.263 · Cited by 4,903
Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1
Barbie, D. A., Tamayo, P., Boehm, J. S., Kim, S. Y., Moody, S. E., Dunn, I. F., Schinzel, A. C., Sandy, P., Meylan, E., Scholl, C., et al. (2009) · Nature · doi:10.1038/nature08460 · Cited by 3,922
Self-citationStratton, M. R., Campbell, P. J., & Futreal, P. A. (2009) · Nature · doi:10.1038/nature07943 · Cited by 3,625
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
Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection.
Li, C., & Wong, W. H. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.98.1.31 · Cited by 3,133
Introduction to Mathematical Statistics.
Aa, Hogg, R. V., & Craig, A. T. (1996) · Journal of the American Statistical Association · doi:10.2307/2291439 · Cited by 2,907
Circular binary segmentation for the analysis of array-based DNA copy number data
Olshen, A. B., Venkatraman, E. S., Lucito, R., & Wigler, M. H. (2004) · Biostatistics · doi:10.1093/biostatistics/kxh008 · Cited by 2,304
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Research works printed but not linked: 2
- NCI and NCBI’s SKY/M-FISH and CGH Database 〈 http://www.ncbi.nlm.nih.gov/sky/skyweb.cgi 〉 (2001)
- Wu, C. & Ponnappan, U. NF-κB Signaling Pathway 〈 http://www.biocarta.com/pathfiles/h_nfkbPathway.asp#contributors 〉 (2009)
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Items 101–133 of 133
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Ke, F., Voss, A., Kerr, J. B., O'Reilly, L. A., Tai, L., Echeverry, N., Bouillet, P., Strasser, A., & Kaufmann, T. (2012) · Cell Death & Differentiation · doi:10.1038/cdd.2011.210 · Cited by 113
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Papatzimas, J. W., Gorobets, E., Maity, R., Muniyat, M. I., MacCallum, J. L., Neri, P., Bahlis, N. J., & Derksen, D. J. (2019) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.9b00455 · Cited by 103
Integrative multi-omics module network inference with lemon-tree
Bonnet, E., Calzone, L., & Michoel, T. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003983 · Cited by 98
Nangia, V., Siddiqui, F. M., Caenepeel, S., Timonina, D., Bilton, S. J., Phan, N., Gomez-Caraballo, M., Archibald, H. L., Li, C., Fraser, C., et al. (2018) · Cancer Discovery · doi:10.1158/2159-8290.cd-18-0277 · Cited by 94
Jeay, S., Ferretti, S., Holzer, P., Fuchs, J., Chapeau, E. A., Wartmann, M., Sterker, D., Romanet, V., Murakami, M., Kerr, G., et al. (2018) · Cancer Research · doi:10.1158/0008-5472.can-18-0338 · Cited by 87
Self-citationYu, D., Liu, Z., Su, C., Han, Y., Duan, X., Zhang, R., Liu, X., Yang, Y., & Xu, S. (2020) · Thoracic Cancer · doi:10.1111/1759-7714.13204 · Cited by 80
Neutralization of terminal differentiation in gliomagenesis
Hu, J., Ho, A. L., Yuan, L., Hu, B., Hua, S., Hwang, S. S., Zhang, J., Hu, T., Zheng, H., Gan, B., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1308610110 · Cited by 76
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Syed, S., Bouchard-Côté, A., Deligiannidis, G., & Doucet, A. (2022) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/rssb.12464 · Cited by 68
Alidousty, C., Baar, T., Martelotto, L. G., Heydt, C., Wagener, S., Fassunke, J., Duerbaum, N., Scheel, A. H., Frank, S., Holz, B., et al. (2018) · The Journal of Pathology · doi:10.1002/path.5110 · Cited by 69
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Tu, Q., Hao, J., Zhou, X., Yan, L., Dai, H., Sun, B., Yang, D., An, S., Lv, L., Jiao, B., et al. (2018) · Oncogene · doi:10.1038/onc.2017.316 · Cited by 66
Bok is a genuine multi-BH-domain protein that triggers apoptosis in the absence of Bax and Bak
Einsele-Scholz, S., Malmsheimer, S., Bertram, K., Stehle, D., Johänning, J., Manz, M., Daniel, P. T., Gillissen, B. F., Schulze-Osthoff, K., & Essmann, F. (2016) · Journal of Cell Science · doi:10.1242/jcs.181727 · Cited by 65
Macdonald, J. D., Chacón Simon, S., Han, C., Wang, F., Shaw, J. G., Howes, J. E., Sai, J., Yuh, J. P., Camper, D., Alicie, B. M., et al. (2019) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.9b01411 · Cited by 66
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Shimizu, K., Gi, M., Suzuki, S., North, B. J., Watahiki, A., Fukumoto, S., Asara, J. M., Tokunaga, F., Wei, W., & Inuzuka, H. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109988 · Cited by 62
Allosteric inhibition of antiapoptotic MCL-1
Lee, S., Wales, T. E., Escudero, S., Cohen, D. T., Luccarelli, J., Gallagher, C. G., Cohen, N. A., Huhn, A. J., Bird, G. H., Engen, J. R., et al. (2016) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3223 · Cited by 59
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Liu, X., Ding, C., Tan, W., & Zhang, A. (2020) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2020.107516 · Cited by 54
BCL-XL is crucial for progression through the adenoma-to-carcinoma sequence of colorectal cancer
Ramesh, P., Lannagan, T. R. M., Jackstadt, R., Atencia Taboada, L., Lansu, N., Wirapati, P., van Hooff, S. R., Dekker, D., Pritchard, J., Kirov, A. B., et al. (2021) · Cell Death & Differentiation · doi:10.1038/s41418-021-00816-w · Cited by 52
Hughesman, C. B., Lu, X. J. D., Liu, K. Y. P., Zhu, Y., Poh, C. F., & Haynes, C. (2016) · PLOS ONE · doi:10.1371/journal.pone.0161274 · Cited by 46
Histone Lysine Methylation Dynamics Control EGFR DNA Copy-Number Amplification
Clarke, T. L., Tang, R., Chakraborty, D., Van Rechem, C., Ji, F., Mishra, S., Ma, A., Kaniskan, H. Ü., Jin, J., Lawrence, M. S., et al. (2020) · Cancer Discovery · doi:10.1158/2159-8290.cd-19-0463 · Cited by 50
Self-citationStover, E. H., Baco, M. B., Cohen, O., Li, Y. Y., Christie, E. L., Bagul, M., Goodale, A., Lee, Y., Pantel, S., Rees, M. G., et al. (2019) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-18-1243 · Cited by 49
Self-citationRawat, V., Malvi, P., Della Manna, D., Yang, E. S., Bugide, S., Zhang, X., Gupta, R., & Wajapeyee, N. (2021) · Oncogene · doi:10.1038/s41388-021-01683-y · Cited by 43
Mazzucco, A. E., Smogorzewska, A., Kang, C., Luo, J., Schlabach, M. R., Xu, Q., Patel, R., & Elledge, S. J. (2017) · Genes & Development · doi:10.1101/gad.304857.117 · Cited by 35
Liu, Y., Li, Y., Wang, X., Liu, F., Gao, P., Quinn, M. M., Li, F., Merlino, A. A., Benes, C., Liu, Q., et al. (2017) · Cancer Research · doi:10.1158/0008-5472.can-17-0567 · Cited by 33
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Conage‐Pough, J. E., & Boise, L. H. (2018) · The FEBS Journal · doi:10.1111/febs.14505 · Cited by 32
Glutamine deprivation counteracts hypoxia-induced chemoresistance
Wappler, J., Arts, M., Röth, A., Heeren, R. M. A., Peter Neumann, U., Olde Damink, S. W., Soons, Z., & Cramer, T. (2020) · Neoplasia · doi:10.1016/j.neo.2019.10.004 · Cited by 34
Formation of a structurally-stable conformation by the intrinsically disordered MYC:TRRAP complex
Feris, E. J., Hinds, J. W., & Cole, M. D. (2019) · PLOS ONE · doi:10.1371/journal.pone.0225784 · Cited by 29
Comparative analysis of algorithms for integration of copy number and expression data
Louhimo, R., Lepikhova, T., Monni, O., & Hautaniemi, S. (2012) · Nature Methods · doi:10.1038/nmeth.1893 · Cited by 30
Regulation of cellular senescence by microRNAs
Ma, X., Zheng, Q., Zhao, G., Yuan, W., & Liu, W. (2020) · Mechanisms of Ageing and Development · doi:10.1016/j.mad.2020.111264 · Cited by 30
Integrated genomic analyses of ovarian carcinoma
The Cancer Genome Atlas Research Network (2011) · Nature · doi:10.1038/nature10166 · Cited by 129
Wang, Y., Liu, S., Chen, Y., Zhu, B., & Xing, Q. (2022) · World Journal of Oncology · doi:10.14740/wjon1446 · Cited by 17
Schaafsma, E., Zhao, Y., Zhang, L., Li, Y., & Cheng, C. (2021) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-20-0526 · Cited by 12
Metadata
- Authors
- Beroukhim, R., Mermel, C. H., Porter, D., Wei, G., Raychaudhuri, S., Donovan, J., Barretina, J., Boehm, J. S., Dobson, J., Urashima, M., Mc Henry, K. T., Pinchback, R. M., Ligon, A. H., Cho, Y.-J., Haery, L., Greulich, H., Reich, M., Winckler, W., Lawrence, M. S., Weir, B. A., Tanaka, K. E., Chiang, D. Y., Bass, A. J., Loo, A., Hoffman, C., Prensner, J., Liefeld, T., Gao, Q., Yecies, D., Signoretti, S., Maher, E., Kaye, F. J., Sasaki, H., Tepper, J. E., Fletcher, J. A., Tabernero, J., Baselga, J., Tsao, M.-S., Demichelis, F., Rubin, M. A., Janne, P. A., Daly, M. J., Nucera, C., Levine, R. L., Ebert, B. L., Gabriel, S., Rustgi, A. K., Antonescu, C. R., Ladanyi, M., Letai, A., Garraway, L. A., Loda, M., Beer, D. G., True, L. D., Okamoto, A., Pomeroy, S. L., Singer, S., Golub, T. R., Lander, E. S., Getz, G., Sellers, W. R., & Meyerson, M.
- Affiliations
- Broad Institute (US)
- Jikei University School of Medicine (JP)
- Brigham and Women's Hospital (US)
- Boston Children's Hospital (US)
- Dana-Farber Cancer Institute (US)
- The University of Texas Southwestern Medical Center (US)
- Walter Reed National Military Medical Center (US)
- Nagoya City University (JP)
- University of North Carolina at Chapel Hill (US)
- Universitat Autònoma de Barcelona (ES)
- University Health Network (CA)
- Weill Cornell Medicine (US)
- Beth Israel Deaconess Medical Center (US)
- Memorial Sloan Kettering Cancer Center (US)
- Abramson Cancer Center (US)
- University of Michigan (US)
- University of Washington Medical Center (US)
- Corresponding author
- Lander, Eric S.
- Getz, Gad
- Sellers, William R.
- Meyerson, Matthew
- ORCID
- Beroukhim, Rameen
- Mermel, Craig H.
- Raychaudhuri, Soumya
- Donovan, Jerry
- Barretina, Jordi
- Boehm, Jesse S.
- Urashima, Mitsuyoshi
- Ligon, Azra H.
- Cho, Yoon-Jae
- Greulich, Heidi
- Reich, Michael
- Winckler, Wendy
- Lawrence, Michael S.
- Tanaka, Kumiko E.
- Chiang, Derek Y.
- Bass, Adam J.
- Hoffman, Carter
- Prensner, John
- Liefeld, Ted
- Gao, Qing
- Yecies, Derek
- Signoretti, Sabina
- Maher, Elizabeth
- Kaye, Frederic J.
- Tepper, Joel E.
- Fletcher, Jonathan A.
- Tabernero, Josep
- Tsao, Ming-Sound
- Demichelis, Francesca
- Rubin, Mark A.
- Janne, Pasi A.
- Daly, Mark J.
- Nucera, Carmelo
- Levine, Ross L.
- Ebert, Benjamin L.
- Gabriel, Stacey
- Rustgi, Anil K.
- Antonescu, Cristina R.
- Ladanyi, Marc
- Letai, Anthony
- Garraway, Levi A.
- Loda, Massimo
- Beer, David G.
- True, Lawrence D.
- Okamoto, Aikou
- Pomeroy, Scott L.
- Singer, Samuel
- Golub, Todd R.
- Lander, Eric S.
- Getz, Gad
- Sellers, William R.
- Meyerson, Matthew
- Venue
- Nature
- Published
- 2010-02
- Volume
- 463
- Issue
- 7283
- Pages
- 899-905
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2826709
- OpenAlex
- W2153056550
- Cited by
- 4,017
- References
- 98
- Citations by year
- 2026: 160 · 2025: 215 · 2024: 268 · 2023: 257 · 2022: 266 · 2021: 287 · 2020: 283 · 2019: 222 · 2018: 278 · 2017: 261 · 2016: 253 · 2015: 262 · 2014: 232 · 2013: 278 · 2012: 221
- FWCI
- 77.79
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- Institutional Research Information System (Università degli Studi di Trento) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- National Human Genome Research Institute (U54HG003067)
- National Cancer Institute (P50CA90578, K08CA134931, R01CA109038, P01CA098101, P01CA085859, U24CA126546, R01CA109467, P50CA090578, K08CA122833)
- National Institute of General Medical Sciences (T32GM007753)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (K08AR055688)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- somatic copy number alterations, focal copy number alterations, cancer genomics, Mcl-1, Bcl-xL, Bcl-2 family proteins, apoptosis, NF-κB signaling, anti-apoptotic genes, oncogene amplification, fragile sites, homozygous deletion, hemizygous deletion
- MeSH terms
- Cell Survival, Gene Amplification, Multigene Family, Humans, Neoplasms, Signal Transduction, Apoptosis, Gene Dosage, Proto-Oncogene Proteins c-bcl-2, Genomics, Cell Line, Tumor, bcl-X Protein, DNA Copy Number Variations, Myeloid Cell Leukemia Sequence 1 Protein
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