The landscape of somatic copy-number alteration across human cancers

Nature - Tập 463 Số 7283 - Trang 899-905 - 2010
Rameen Beroukhim1, Craig H. Mermel1, Dale Porter2, Wei Guo1, Soumya Raychaudhuri1, Jerry Donovan2, Jordi Barretina1, Jesse S. Boehm1, Jennifer Dobson1, Mitsuyoshi Urashima3, Kevin T. Mc Henry2, Reid M. Pinchback1, Azra H. Ligon4, Yoon‐Jae Cho5, Leila Haery1, Heidi Greulich1, Michael Reich1, Wendy Winckler1, Michael S. Lawrence1, Barbara A. Weir1, Kumiko Tanaka1, Derek Y. Chiang1, Adam J. Bass1, Alice Loo2, Carter Hoffman6, John R. Prensner6, Ted Liefeld1, Qing Gao1, Derek Yecies6, Sabina Signoretti6, Elizabeth A. Maher7, Frederic J. Kaye8, Hidefumi Sasaki9, Joel E. Tepper10, Jonathan A. Fletcher4, Josep Tabernero11, José Baselga11, Ming‐Sound Tsao12, Francesca Demichelis13, Mark A. Rubin13, Pasi A. Jänne6, Mark J. Daly1, Carmelo Nucera14, Ross L. Levine15, Benjamin L. Ebert4, Stacey Gabriel1, Anil K. Rustgi16, Cristina R. Antonescu15, Marc Ladanyi15, Anthony Letai6, Levi A. Garraway6, Massimo Loda4, David G. Beer17, Lawrence D. True18, Aikou Okamoto19, Scott L. Pomeroy5, Samuel Singer15, Todd R. Golub6, Sı́lvia Beà20, Gad Getz1, William R. Sellers2, Matthew Meyerson20
1Cancer Program and Medical and Population Genetics Group, The Broad Institute of M.I.T. and Harvard, 7 Cambridge Center,,
2Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA ,
3Division of Molecular Epidemiology, Jikei University School of Medicine, 3-25-8 Nishi-shimbashi, Minato-ku, Tokyo 105-8461, Japan,
4Departments of Medicine and Pathology, Brigham and Women’s Hospital, 75 Francis Street,
5Department of Neurology, Children’s Hospital Boston, 300 Longwood Avenue,
6Departments of Medical Oncology, Pediatric Oncology, and Cancer Biology, and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, 44 Binney Street,
7Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas 75390-9186, USA,
8Genetics Branch, Center for Cancer Research, National Cancer Institute and National Naval Medical Center, Bethesda, Maryland 20889, USA ,
9Department of Surgery II, Nagoya City University Medical School, Nagoya, 467-8601, Japan
10Department of Genetics and Radiation Oncology, UNC/Lineberger Comprehensive Cancer Center, University of North Carolina, School of Medicine, Chapel Hill, North Carolina 27599, USA,
11Medical Oncology Program, Vall d’Hebron University Hospital Research Institute, Vall d’Hebron Institute of Oncology, and Autonomous University of Barcelona, 08035 Barcelona, Spain
12Department of Pathology and Division of Applied Molecular Oncology, University Health Network, Princess Margaret Hospital and Ontario Cancer Institute, Toronto, Ontario M5G 2M9, Canada,
13Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York 10065, USA,
14Department of Pathology, Beth Israel Deaconess Medical Center, 3 Blackfan Circle, Boston, Massachusetts 02115, USA,
15Departments of Medicine and Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA,
16Departments of Medicine (GI Division) and Genetics, and Abramson Cancer Center, University of Pennsylvania, 415 Curie Boulevard, Philadelphia, Pennsylvania 19104, USA,
17Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, Ann Arbor, Michigan 48109, USA,
18Department of Pathology, University of Washington Medical Center, 1959 North East Pacific Street, Seattle, Washington 98195-6100, USA,
19Department of Obstetrics and Gynecology, Jikei University School of Medicine 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
20Departments of Medicine, Pathology, Pediatrics, and Systems Biology, Harvard Medical School, 25 Shattuck Street,

Tóm tắt

Từ khóa


Tài liệu tham khảo

Futreal, P. A. et al. A census of human cancer genes. Nature Rev. Cancer 4, 177–183 (2004)

Stuart, D. & Sellers, W. R. Linking somatic genetic alterations in cancer to therapeutics. Curr. Opin. Cell Biol. 21, 304–310 (2009)

Stratton, M. R., Campbell, P. J. & Futreal, P. A. The cancer genome. Nature 458, 719–724 (2009)

Baudis, M. Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data. BMC Cancer 7, 226 (2007)

Mitelman Database of Chromosome Aberrations in Cancer (eds Mitelman, F. Johansson, B. and Mertens, F.) 〈 http://cgap.nci.nih.gov/Chromosomes/Mitelman 〉 (2009)

NCI and NCBI’s SKY/M-FISH and CGH Database 〈 http://www.ncbi.nlm.nih.gov/sky/skyweb.cgi 〉 (2001)

Weir, B. A. et al. Characterizing the cancer genome in lung adenocarcinoma. Nature 450, 893–898 (2007)

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)

Lahortiga, I. et al. Duplication of the MYB oncogene in T cell acute lymphoblastic leukemia. Nature Genet. 39, 593–595 (2007)

Zender, L. et al. Identification and validation of oncogenes in liver cancer using an integrative oncogenomic approach. Cell 125, 1253–1267 (2006)

Mullighan, C. G. et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 446, 758–764 (2007)

Wiedemeyer, R. et al. Feedback circuit among INK4 tumor suppressors constrains human glioblastoma development. Cancer Cell 13, 355–364 (2008)

Cancer_Genome_Atlas_Research_Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061–1068 (2008)

Chitale, D. et al. An integrated genomic analysis of lung cancer reveals loss of DUSP4 in EGFR-mutant tumors. Oncogene 28, 2773–2783 (2009)

GlaxoSmithKline. GSK Cancer Cell Line Genomic Profiling Data 〈 https://cabig.nci.nih.gov/tools/caArray_GSKdata 〉 (2008)

Mullighan, C. G. et al. BCR-ABL1 lymphoblastic leukaemia is characterized by the deletion of Ikaros. Nature 453, 110–114 (2008)

Mazzarella, R. & Schlessinger, D. Pathological consequences of sequence duplications in the human genome. Genome Res. 8, 1007 (1998)

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)

Garraway, L. A. et al. Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 436, 117–122 (2005)

Raychaudhuri, S. et al. Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. PLoS Genet. 5, e1000534 (2009)

Letai, A. G. Diagnosing and exploiting cancer’s addiction to blocks in apoptosis. Nature Rev. Cancer 8, 121–132 (2008)

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)

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)

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)

Rampino, N. et al. Somatic frameshift mutations in the BAX gene in colon cancers of the microsatellite mutator phenotype. Science 275, 967–969 (1997)

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)

Wu, C. & Ponnappan, U. NF-κB Signaling Pathway 〈 http://www.biocarta.com/pathfiles/h_nfkbPathway.asp#contributors 〉 (2009)

Boehm, J. S. et al. Integrative genomic approaches identify IKBKE as a breast cancer oncogene. Cell 129, 1065–1079 (2007)

Barbie, D. A. et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature 462, 108–112 (2009)

Scholl, C. et al. Synthetic lethal interaction between oncogenic KRAS dependency and suppression of STK33 in human cancer cells. Cell 137, 821–834 (2009)

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)

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)

Luo, B. et al. Highly parallel identification of essential genes in cancer cells. Proc. Natl Acad. Sci. USA 105, 20380–20385 (2008)

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)

Lin, W. M. et al. Modeling genomic diversity and tumor dependency in malignant melanoma. Cancer Res. 68, 664–673 (2008)

Tonon, G. et al. High-resolution genomic profiles of human lung cancer. Proc. Natl Acad. Sci. USA 102, 9625–9630 (2005)

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)

Spits, C. et al. Recurrent chromosomal abnormalities in human embryonic stem cells. Nature Biotechnol. 26, 1361–1363 (2008)

Lefort, N. et al. Human embryonic stem cells reveal recurrent genomic instability at 20q11.21. Nature Biotechnol. 26, 1364–1366 (2008)

Fanidi, A., Harrington, E. A. & Evan, G. I. Cooperative interaction between c-myc and bcl-2 proto-oncogenes. Nature 359, 554–556 (1992)

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)

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)

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)

Myllykangas, S., Bohling, T. & Knuutila, S. Specificity, selection and significance of gene amplifications in cancer. Semin. Cancer Biol. 17, 42–55 (2007)

Albertson, D. G. Gene amplification in cancer. Trends Genet. 22, 447–455 (2006)

Fukasawa, K. Centrosome amplification, chromosome instability and cancer development. Cancer Lett. 230, 6–19 (2005)

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)

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)

Lundberg, A. S. et al. Immortalization and transformation of primary human airway epithelial cells by gene transfer. Oncogene 21, 4577–4586 (2002)

Thông tin
Thông tin xuất bản

Nature

Tập 463 Số 7283

899-905

Thông tin tác giả