Cited by 709Cancer Genomics and DiagnosticsGenomic variations and chromosomal abnormalitiesChromatin Remodeling and Cancer

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Signatures of mutation and selection in the cancer genome

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Bignell, Graham R., Greenman, Chris D., Davies, Helen, Butler, Adam P., Edkins, Sarah, Andrews, Jenny M., Buck, Gemma, Chen, Lina, Beare, David, Latimer, Calli, Widaa, Sara, Hinton, Jonathon, Fahey, Ciara, Fu, Beiyuan, Swamy, Sajani, Dalgliesh, Gillian L., Teh, Bin T., Deloukas, Panos, Yang, Fengtang, Campbell, Peter J., Futreal, P. Andrew, Stratton, Michael R.·2010·Nature

DOI 10.1038/nature08768PMC PMC3145113

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Abstract

The cancer genome is moulded by the dual processes of somatic mutation and selection. Homozygous deletions in cancer genomes occur over recessive cancer genes, where they can confer selective growth advantage, and over fragile sites, where they are thought to reflect an increased local rate of DNA breakage. However, most homozygous deletions in cancer genomes are unexplained. Here we identified 2,428 somatic homozygous deletions in 746 cancer cell lines. These overlie 11% of protein-coding genes that, therefore, are not mandatory for survival of human cells. We derived structural signatures that distinguish between homozygous deletions over recessive cancer genes and fragile sites. Application to clusters of unexplained homozygous deletions suggests that many are in regions of inherent fragility, whereas a small subset overlies recessive cancer genes. The results illustrate how structural signatures can be used to distinguish between the influences of mutation and selection in cancer genomes. The extensive copy number, genotyping, sequence and expression data available for this large series of publicly available cancer cell lines renders them informative reagents for future studies of cancer biology and drug discovery. Two Articles in this issue add major data sets to the growing picture of the cancer genome. Bignell et al. analysed a large number of homozygous gene deletions in a collection of 746 publicly available cancer cell lines. Combined with information about hemizygous deletions of the same genes, the data suggest that many deletions found in cancer reflect the position of a gene at a fragile site in the genome, rather than as a recessive cancer gene whose loss confers a selective growth advantage. Beroukhim et al. present the largest data set to date on somatic copy-number variations across more than 3,000 specimens of human primary cancers. Many alterations are shared between multiple tumour types. Functional experiments demonstrate an oncogenic role for the apoptosis genes MCL1 and BCL2L1 that are associated with amplifications found in many cancers. Homozygous gene deletions in cancer cells occur over recessive cancer genes (where they can confer selective growth advantage) or over genes at fragile sites of the genome (where they are thought to reflect increased DNA breakage). Here, a large number of homozygous deletions in a collection of cancer cell lines are identified and analysed to derive structural signatures for the two different types of deletion. More deletions are found in inherently fragile regions, and fewer overlying recessive genes.

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A TARBP2 mutation in human cancer impairs microRNA processing and DICER1 function
Melo, S. A., Ropero, S., Moutinho, C., Aaltonen, L. A., Yamamoto, H., Calin, G. A., Rossi, S., Fernández, A. F., Carneiro, F., Oliveíra, C., et al. (2009) · Nature Genetics · doi:10.1038/ng.317 · Cited by 375
Retracted
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
PTEN , a Putative Protein Tyrosine Phosphatase Gene Mutated in Human Brain, Breast, and Prostate Cancer
Li, J., Yen, C., Liaw, D., Podsypanina, K., Bose, S., Wang, S. I., Puc, J., Miliaresis, C., Rodgers, L., McCombie, R., et al. (1997) · Science · doi:10.1126/science.275.5308.1943 · Cited by 4,785
The cancer genome
Stratton, M. R., Campbell, P. J., & Futreal, P. A. (2009) · Nature · doi:10.1038/nature07943 · Cited by 3,625
Self-citation
The Consensus Coding Sequences of Human Breast and Colorectal Cancers
Sjöblom, T., Jones, S., Wood, L. D., Parsons, D. W., Lin, J., Barber, T. D., Mandelker, D. L., Leary, R. J., Ptak, J., Silliman, N., et al. (2006) · Science · doi:10.1126/science.1133427 · Cited by 3,161
Somatic mutations affect key pathways in lung adenocarcinoma
Ding, L., Getz, G., Wheeler, D. A., Mardis, E. R., McLellan, M. D., Cibulskis, K., Sougnez, C., Greulich, H., Muzny, D. M., Morgan, M. B., et al. (2008) · Nature · doi:10.1038/nature07423 · Cited by 2,681
Inactivation of the Type II TGF-β Receptor in Colon Cancer Cells with Microsatellite Instability
Markowitz, S. D., Wang, J., Myeroff, L. L., Parsons, R. E., Sun, L., Lutterbaugh, J., Fan, R. S., Zborowska, E., Kinzler, K. W., Vogelstein, B., et al. (1995) · Science · doi:10.1126/science.7761852 · Cited by 2,267
Activation of the DNA damage checkpoint and genomic instability in human precancerous lesions
Gorgoulis, V. G., Vassiliou, L.-V. F., Karakaidos, P., Zacharatos, P., Kotsinas, A., Liloglou, T., Venere, M., DiTullio, R. A., Kastrinakis, N. G., Levy, B., et al. (2005) · Nature · doi:10.1038/nature03485 · Cited by 2,009
Truncating mutations of hSNF5/INI1 in aggressive paediatric cancer
Versteege, I., Sévenet, N., Lange, J., Rousseau-Merck, M.-F., Ambros, P. F., Handgretinger, R., Aurias, A., & Delattre, O. (1998) · Nature · doi:10.1038/28212 · Cited by 1,552
The cytoplasmic domain of the cell adhesion molecule uvomorulin associates with three independent proteins structurally related in different species.
Ozawa, M., Baribault, H., & Kemler, R. (1989) · The EMBO Journal · doi:10.1002/j.1460-2075.1989.tb03563.x · Cited by 1,396

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Mosig, R., Lin, L., Senturk, E., Shah, H., Huang, F., Schlosshauer, P. W., Cohen, S., Fruscio, R., Marchini, S., D’Incalci, M., et al. (2012) · Journal of Ovarian Research · doi:10.1186/1757-2215-5-4 · Cited by 21
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Fischer, A., Greenman, C., & Mustonen, V. (2011) · Genetics · doi:10.1534/genetics.111.127480 · Cited by 20
Self-citation
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Saldivar, J. C., & Park, D. (2018) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22684 · Cited by 20
Molecular Pathway Analysis of Mutation Data for Biomarkers Discovery and Scoring of Target Cancer Drugs
Zolotovskaia, M., Sorokin, M., Garazha, A., Borisov, N., & Buzdin, A. A. (2019) · Methods in molecular biology · doi:10.1007/978-1-0716-0138-9_16 · Cited by 20
Selective pericentromeric heterochromatin dismantling caused by TP53 activation during senescence
Méndez-Bermúdez, A., Lototska, L., Pousse, M., Tessier, F., Croce, O., Latrick, C. M., Cherdyntseva, V., Nassour, J., Xiaohua, J., Lu, Y., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac603 · Cited by 23
Methylation-mediated silencing of PTPRD induces pulmonary hypertension by promoting pulmonary arterial smooth muscle cell migration via the PDGFRB/PLCγ1 axis
Xu, J., Zhong, Y., Yin, H., Linneman, J., Luo, Y., Xia, S., Xia, Q., Yang, L., Huang, X., Kang, K., et al. (2022) · Journal of Hypertension · doi:10.1097/hjh.0000000000003220 · Cited by 20
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Wang, N., Xu, S., & Egli, D. M. (2023) · Trends in Cell Biology · doi:10.1016/j.tcb.2023.03.015 · Cited by 21
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Woodward, E. L., Biloglav, A., Ravi, N., Yang, M., Ekblad, L., Wennerberg, J. P., & Paulsson, K. M. (2017) · Endocrine Related Cancer · doi:10.1530/erc-16-0522 · Cited by 20
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Sinai, M. I., & Kerem, B. (2018) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22715 · Cited by 22
gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data
Ciccolella, S., Soto, M., Patterson, M., Vedova, G. D., Hajirasouliha, I., & Bonizzoni, P. (2020) · BMC Bioinformatics · doi:10.1186/s12859-020-03736-7 · Cited by 22
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Liu, Y., Sun, P., Zhao, Y., & Liu, B. (2020) · Hematological Oncology · doi:10.1002/hon.2776 · Cited by 19
Processing DNA lesions during mitosis to prevent genomic instability
Audrey, A., de Haan, L., van Vugt, M. A. T. M., & de Boer, H. R. (2022) · Biochemical Society Transactions · doi:10.1042/bst20220049 · Cited by 20
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Whole genome profiling and other high throughput technologies in lymphoid neoplasms—current contributions and future hopes
Campo, E. (2013) · Modern Pathology · doi:10.1038/modpathol.2012.179 · Cited by 20
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Newman, S., Howarth, K., Greenman, C., Bignell, G. R., Tavaré, S., & Edwards, P. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0064991 · Cited by 19
Self-citation
Transcription-replication conflicts at chromosomal fragile sites—consequences in M phase and beyond
Oestergaard, V. H., & Lisby, M. (2016) · Chromosoma · doi:10.1007/s00412-016-0617-2 · Cited by 19
Synthetic whole-slide image tile generation with gene expression profile-infused deep generative models
Carrillo‐Pérez, F., Pizurica, M., Ozawa, M. G., Vogel, H. S., West, R. B., Kong, C. S., Herrera, L. J., Shen, J., & Gevaert, O. (2023) · Cell Reports Methods · doi:10.1016/j.crmeth.2023.100534 · Cited by 19
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Rosen, D. M., Younkin, E. M., Miller, S. D., & Casper, A. M. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003817 · Cited by 19
Discovery and analysis of consistent active sub-networks in cancers
Gaire, R., Smith, L. K., Humbert, P. O., Bailey, J., Stuckey, P. J., & Haviv, I. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-s2-s7 · Cited by 18
Retinoblastoma tumor suppressor functions shared by stem cell and cancer cell strategies
Kohno, S., Kitajima, S., Sasaki, N., & Takahashi, C. (2016) · World Journal of Stem Cells · doi:10.4252/wjsc.v8.i4.170 · Cited by 18
Coordinating Replication with Transcription
Achar, Y. J., & Foiani, M. (2017) · Advances in experimental medicine and biology · doi:10.1007/978-981-10-6955-0_20 · Cited by 18
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Savelyeva, L., & Brueckner, L. M. (2014) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-014-1723-z · Cited by 18
Fhit and Wwox loss-associated genome instability: A genome caretaker one-two punch
Schrock, M. S., Karras, J. R., Guggenbiller, M. J., Druck, T., Batar, B., & Huebner, K. (2016) · Advances in Biological Regulation · doi:10.1016/j.jbior.2016.09.008 · Cited by 17
H2A Histone Family Member X (H2AX) Is Upregulated in Ovarian Cancer and Demonstrates Utility as a Prognostic Biomarker in Terms of Overall Survival
Saravi, S., Katsuta, E., Jeyaneethi, J., Amin, H. A., Kaspar, M., Takabe, K., Pados, G., Drenos, F., Hall, M., & Karteris, E. (2020) · Journal of Clinical Medicine · doi:10.3390/jcm9092844 · Cited by 17
Association between the copy number variation ofCCSER1gene and growth traits in ChineseCapra hircus(goat) populations
Xu, Z., Wang, X., Song, X., An, Q., Wang, D., Zhang, Z., Ding, X., Yao, Z., Wang, E., Liu, X., et al. (2022) · Animal Biotechnology · doi:10.1080/10495398.2022.2025818 · Cited by 17
Novel insights into the pathogenesis of follicular lymphoma by molecular profiling of localized and systemic disease forms
Kalmbach, S., Grau, M., Zapukhlyak, M., Leich, E., Jurinović, V., Hoster, E., Staiger, A. M., Kurz, K. S., Weigert, O., Gaitzsch, E., et al. (2023) · Leukemia · doi:10.1038/s41375-023-01995-w · Cited by 17
ABSOLUTE cancer genomics
Loo, P. V., & Campbell, P. J. (2012) · Nature Biotechnology · doi:10.1038/nbt.2293 · Cited by 17
Self-citation
Human B-cell cancer cell lines as a preclinical model for studies of drug effect in diffuse large B-cell lymphoma and multiple myeloma
Laursen, M. B., Falgreen, S., Bødker, J. S., Schmitz, A., Kjeldsen, M. K., Sørensen, S., Madsen, J., El‐Galaly, T. C., Bøgsted, M., Dybkær, K., et al. (2014) · Experimental Hematology · doi:10.1016/j.exphem.2014.07.263 · Cited by 16
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Pandareesh, M. D., Kameshwar, V. H., & Byrappa, K. (2020) · Endocrine Metabolic & Immune Disorders - Drug Targets · doi:10.2174/1871530320666200719020709 · Cited by 17
Pharmacologically targetable vulnerability in prostate cancer carrying RB1-SUCLA2 deletion
Kohno, S., Linn, P., Nagatani, N., Watanabe, Y., Kumar, S., Soga, T., & Takahashi, C. (2020) · Oncogene · doi:10.1038/s41388-020-1381-6 · Cited by 18
The impact of transcription-mediated replication stress on genome instability and human disease
Gnan, S., Liu, Y., Spagnuolo, M., & Chen, C.-L. (2020) · Genome Instability & Disease · doi:10.1007/s42764-020-00021-y · Cited by 16

Authors: Bignell, G. R., Greenman, C. D., Davies, H., Butler, A. P., Edkins, S., Andrews, J. M., Buck, G., Chen, L., Beare, D., Latimer, C., Widaa, S., Hinton, J., Fahey, C., Fu, B., Swamy, S., Dalgliesh, G. L., Teh, B. T., Deloukas, P., Yang, F., Campbell, P. J., Futreal, P. A., & Stratton, M. R.
Affiliations: Wellcome Sanger Institute (GB)
Van Andel Institute (US)
Institute of Cancer Research (GB)
Corresponding author: Futreal, P. Andrew
Stratton, Michael R.
ORCID: Greenman, Chris D.
Davies, Helen
Edkins, Sarah
Buck, Gemma
Chen, Lina
Latimer, Calli
Widaa, Sara
Fu, Beiyuan
Dalgliesh, Gillian L.
Teh, Bin T.
Deloukas, Panos
Yang, Fengtang
Campbell, Peter J.
Futreal, P. Andrew
Stratton, Michael R.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2010-02
Volume: 463
Issue: 7283
Pages: 893-898
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature08768
PMC: PMC3145113
OpenAlex: W2071734901
Cited by: 707
References: 41
Citations by year: 2026: 7 · 2025: 24 · 2024: 21 · 2023: 29 · 2022: 25 · 2021: 32 · 2020: 40 · 2019: 30 · 2018: 44 · 2017: 44 · 2016: 47 · 2015: 48 · 2014: 61 · 2013: 71 · 2012: 76
FWCI: 25.43
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by-nc-sa
creativecommons.org/licenses/by-nc-sa/3.0/ (tdm)
Locations: Nature (publishedVersion, cc-by-nc-sa)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
RePEc: Research Papers in Economics (submittedVersion)
UEA Digital Repository (University of East Anglia) (submittedVersion)
Funders: Wellcome Trust (077012/Z/05/Z, 088340, 093867)
National Cancer Institute (P01CA155258)
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: fragile sites, copy number variation, cancer cell lines, structural signatures, DNA breakage, Mcl-1, Bcl-xL, gene amplification, tumor suppressor
MeSH terms: Chromosomes, Human, DNA Mutational Analysis, Genes, Recessive, Homozygote, Humans, Models, Genetic, Neoplasms, Selection, Genetic, Reproducibility of Results, Genome, Human, Gene Deletion, Gene Dosage, Physical Chromosome Mapping, Oligonucleotide Array Sequence Analysis, Chromosome Fragile Sites, Cell Line, Tumor, Genes, Neoplasm, DNA Copy Number Variations

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