The landscape of somatic copy-number alteration across human cancers

Nature

Volumn 463, Issue 7283, 2010, Pages 899-905

  Beroukhim, Rameen ^a,c,d,e   Mermel, Craig H ^a,c   Porter, Dale ^h   Wei, Guo ^a   Raychaudhuri, Soumya ^a,d   Donovan, Jerry ^h   Barretina, Jordi ^a,c   Boehm, Jesse S ^a   Dobson, Jennifer ^a,c   Urashima, Mitsuyoshi ⁱ   McHenry, Kevin T ^h   Pinchback, Reid M ^a   Ligon, Azra H ^d   Cho, Yoon Jae ^f   Haery, Leila ^a,c   Greulich, Heidi ^a,c,d,e   Reich, Michael ^a   Winckler, Wendy ^a   Lawrence, Michael S ^a   Weir, Barbara A ^a,c   Tanaka, Kumiko E ^a,c   Chiang, Derek Y ^a,c,m   Bass, Adam J ^a,c,d   Loo, Alice ^h   Hoffman, Carter ^a,c   Prensner, John ^a,c   Liefeld, Ted ^a   Gao, Qing ^a   Yecies, Derek ^c   Signoretti, Sabina ^c,d   Maher, Elizabeth ^j   Kaye, Frederic J ^k   Sasaki, Hidefumi ^l   Tepper, Joel E ^m   Fletcher, Jonathan A ^d   Tabernero, Josep ⁿ   Baselga, José ⁿ   Tsao, Ming Sound ^o   Demichelis, Francesca ^p   Rubin, Mark A ^p   Janne, Pasi A ^c,d   Daly, Mark J ^a,q   Nucera, Carmelo ^g   Levine, Ross L ^r   Ebert, Benjamin L ^a,d,e   Gabrie, Stacey ^k   Rustgi, Anil K ^s   Antonescu, Cristina R ^r   Ladanyi, Marc ^r   Letai, Anthony ^c   Garraway, Levi A ^a,c   Loda, Massimo ^c,d   Beer, David G ^t   True, Lawrence D ^u   Okamoto, Aikou ⁱ   Pomeroy, Scott L ^f   Singer, Samuel ^r   Golub, Todd R ^a,c,v   Lander, Eric S ^a,b,e   Getz, Gad ^a   Sellers, William R ^h   Meyerson, Matthew ^a,c,e   more..

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^c DANA FARBER CANCER INSTITUTE   (United States)

^d BRIGHAM AND WOMEN S HOSPITAL   (United States)

^e HARVARD MEDICAL SCHOOL   (United States)

^f BOSTON CHILDREN S HOSPITAL   (United States)

^g BETH ISRAEL DEACONESS MEDICAL CENTER   (United States)

^h NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

ⁱ JIKEI UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^j UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^k NATIONAL CANCER INSTITUTE   (United States)

^l NAGOYA CITY UNIV MEDICAL SCHOOL   (Japan)

^m UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

ⁿ HOSPITAL UNIVERSITARI VALL D HEBRON   (Spain)

^o PRINCESS MARGARET HOSPITAL   (Canada)

^p WEILL CORNELL MEDICAL COLLEGE   (United States)

^q MASSACHUSETTS GENERAL HOSPITAL   (United States)

^r MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^s UNIVERSITY OF PENNSYLVANIA   (United States)

^t UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^u UNIVERSITY OF WASHINGTON MEDICAL CENTER   (United States)

^v HOWARD HUGHES MEDICAL INSTITUTE   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; PROTEIN MCL 1;

CANCER; FREQUENCY ANALYSIS; FUNCTIONAL MORPHOLOGY; GENE EXPRESSION; GENETIC ANALYSIS; HISTOLOGY; HUMAN BEHAVIOR; LANDSCAPE; RESOLUTION; SURVIVAL;

ARTICLE; BCL2 GENE; BCL2L1 GENE; CELL SURVIVAL; CONTROLLED STUDY; GENE; GENE AMPLIFICATION; GENE EXPRESSION; HUMAN; HUMAN CELL; MULTIGENE FAMILY; NEOPLASM; PRIORITY JOURNAL; SOMATIC CELL GENETICS; SOMATIC COPY NUMBER ALTERATION;

APOPTOSIS; BCL-X PROTEIN; CELL LINE, TUMOR; CELL SURVIVAL; DNA COPY NUMBER VARIATIONS; GENE AMPLIFICATION; GENE DOSAGE; GENOMICS; HUMANS; MULTIGENE FAMILY; NEOPLASMS; PROTO-ONCOGENE PROTEINS C-BCL-2; SIGNAL TRANSDUCTION;

EID: 77249119762     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature08822     Document Type: Article

References (49)

1. Futreal, P. A. et al. A census of human cancer genes. Nature Rev. Cancer 4, 177-183 (2004).
2. Stuart, D. & Sellers, W. R. Linking somatic genetic alterations in cancer to therapeutics. Curr. Opin. Cell Biol. 21, 304-310 (2009).
3. Stratton, M. R., Campbell, P. J. & Futreal, P. A. The cancer genome. Nature 458, 719-724 (2009).
4. Baudis, M. Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data. BMC Cancer 7, 226 (2007)
5. Mitelman Database of Chromosome Aberrations in Cancer (eds Mitelman, F. Johansson, B. and Mertens, F.) Æhttp://cgap.nci.nih.gov/Chromosomes/ Mitelman (2009)
6. NCI and NCBI's SKY/M-FISH and CGH Database Æhttp://www.ncbi.nlm. nih.gov/ sky/skyweb.cgiæ (2001).
7. Weir, B. A. et al. Characterizing the cancer genome in lung adenocarcinoma. Nature 450, 893-898 (2007).
8. Eder, A. M. et al. Atypical PKCiota contributes to poor prognosis through loss of apical-basal polarity and cyclin E overexpression in ovarian cancer. Proc. Natl Acad. Sci. USA 102, 12519-12524 (2005).
9. Lahortiga, I. et al. Duplication of the MYB oncogene in T cell acute lymphoblastic leukemia. Nature Genet. 39, 593-595 (2007).
10. Zender, L. et al. Identification and validation of oncogenes in liver cancer using an integrative oncogenomic approach. Cell 125, 1253-1267 (2006).
11. Mullighan, C. G. et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 446, 758-764 (2007).
12. Wiedemeyer, R. et al. Feedback circuit among INK4 tumor suppressors constrains human glioblastoma development. Cancer Cell 13, 355-364 (2008).
13. Cancer-Genome-Atlas-Research-Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061-1068 (2008).
14. Chitale, D. et al. An integrated genomic analysis of lung cancer reveals loss of DUSP4 in EGFR-mutant tumors. Oncogene 28, 2773-2783 (2009).
15. GlaxoSmithKline. GSK Cancer Cell Line Genomic Profiling Data Æhttps:// cabig.nci.nih.gov/tools/caArray-GSKdataæ
16. Mullighan, C. G. et al. BCR-ABL1 lymphoblastic leukaemia is characterized by the deletion of Ikaros. Nature 453, 110-114 (2008).
17. Mazzarella, R. & Schlessinger, D. Pathological consequences of sequence duplications in the human genome. Genome Res. 8, 1007 (1998).
18. Beroukhim, R. et al. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc. Natl Acad. Sci. USA 104, 20007-20012 (2007).
19. Garraway, L. A. et al. Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 436, 117-122 (2005).
20. Raychaudhuri, S. et al. Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. PLoS Genet. 5, e1000534 (2009).
21. Letai, A. G. Diagnosing and exploiting cancer's addiction to blocks in apoptosis. Nature Rev. Cancer 8, 121-132 (2008).
22. Tsujimoto, Y., Gorham, J., Cossman, J., Jaffe, E. & Croce, C. M. The t(14;18) chromosome translocations involved in B-cell neoplasms result from mistakes in VDJ joining. Science 229, 1390-1393 (1985).
23. Cleary, M. L. & Sklar, J. Nucleotide sequence of a t(14;18) chromosomal breakpoint in follicular lymphoma and demonstration of a breakpoint-cluster region near a transcriptionally active locus on chromosome 18. Proc. Natl Acad. Sci. USA 82, 7439-7443 (1985).
24. Bakhshi, A. et al. Cloning the chromosomal breakpoint of t(14;18) human lymphomas: clustering around JH on chromosome 14 and near a transcriptional unit on 18. Cell 41, 899-906 (1985).
25. Rampino, N. et al. Somatic frameshift mutations in the BAX gene in colon cancers of the microsatellite mutator phenotype. Science 275, 967-969 (1997).
26. Arena, V., Martini, M., Luongo, M., Capelli, A. & Larocca, L. M. Mutations of the BIK gene in human peripheral B-cell lymphomas. Genes Chromosom. Cancer 38, 91-96 (2003).
27. Wu, C. & Ponnappan, U. NF-kB Signaling Pathway Æhttp://www. biocarta.com/ pathfiles/h-nfkbPathway.asp#contributorsæ (2009).
28. Boehm, J. S. et al. Integrative genomic approaches identify IKBKE as a breast cancer oncogene. Cell 129, 1065-1079 (2007).
29. Barbie, D. A. et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature 462, 108-112 (2009).
30. Scholl, C. et al. Synthetic lethal interaction between oncogenic KRAS dependency and suppression of STK33 in human cancer cells. Cell 137, 821-834 (2009).
31. Nishida, K. & Hirano, T. The role of Gab family scaffolding adapter proteins in the signal transduction of cytokine and growth factor receptors. Cancer Sci. 94, 1029-1033 (2003).
32. Dearth, R. K., Cui, X., Kim, H. J., Hadsell, D. L. & Lee, A. V. Oncogenic transformation by the signaling adaptor proteins insulin receptor substrate (IRS)-1 and IRS-2. Cell Cycle 6, 705-713 (2007).
33. Luo, B. et al. Highly parallel identification of essential genes in cancer cells. Proc. Natl Acad. Sci. USA 105, 20380-20385 (2008).
34. Kendall, J. et al. Oncogenic cooperation and coamplification of developmental transcription factor genes in lung cancer. Proc. Natl Acad. Sci. USA 104, 16663-16668 (2007).
35. Lin, W. M. et al. Modeling genomic diversity and tumor dependency in malignant melanoma. Cancer Res. 68, 664-673 (2008).
36. Tonon, G. et al. High-resolution genomic profiles of human lung cancer. Proc. Natl Acad. Sci. USA 102, 9625-9630 (2005).
37. Smith, L. T. et al. 20q11.1 amplification in giant-cell tumor of bone: Array CGH, FISH, and association with outcome. Genes Chromosom. Cancer 45, 957-966 (2006).
38. Spits, C. et al. Recurrent chromosomal abnormalities in human embryonic stem cells. Nature Biotechnol. 26, 1361-1363 (2008).
39. Lefort, N. et al. Human embryonic stem cells reveal recurrent genomic instability at 20q11.21. Nature Biotechnol. 26, 1364-1366 (2008).
40. Fanidi, A., Harrington, E. A. & Evan, G. I. Cooperative interaction between c-myc and bcl-2 proto-oncogenes. Nature 359, 554-556 (1992).
41. Zhou, P. et al. MCL1 transgenic mice exhibit a high incidence of B-cell lymphoma manifested as a spectrum of histologic subtypes. Blood 97, 3902-3909 (2001).
42. Beverly, L. J. & Varmus, H. E. MYC-induced myeloid leukemogenesis is accelerated by all six members of the antiapoptotic BCL family. Oncogene 28, 1274-1279 (2009).
43. Dal Cin, P. et al. Cytogenetic and fluorescence in situ hybridization investigation of ring chromosomes characterizing a specific pathologic subgroup of adipose tissue tumors. Cancer Genet. Cytogenet. 68, 85-90 (1993).
44. Myllykangas, S., Bohling, T. & Knuutila, S. Specificity, selection and significance of gene amplifications in cancer. Semin. Cancer Biol. 17, 42-55 (2007).
45. Albertson, D. G. Gene amplification in cancer. Trends Genet. 22, 447-455 (2006).
46. Fukasawa, K. Centrosome amplification, chromosome instability and cancer development. Cancer Lett. 230, 6-19 (2005).
47. Smith, D. I., Zhu, Y., McAvoy, S. & Kuhn, R. Common fragile sites, extremely large genes, neural development and cancer. Cancer Lett. 232, 48-57 (2006).
48. Hupé, P., Stransky, N., Thiery, J.-P., Radvanyi, F. & Barillot, E. Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinformatics 20, 3413-3422 (2004).
49. Lundberg, A. S. et al. Immortalization and transformation of primary human airway epithelial cells by gene transfer. Oncogene 21, 4577-4586 (2002).