Complex landscapes of somatic rearrangement in human breast cancer genomes (original) (raw)
References
- Kaye, F. J. Mutation-associated fusion cancer genes in solid tumors. Mol. Cancer Ther. 8, 1399–1408 (2009)
Article CAS Google Scholar - Mitelman, F., Johansson, B. & Mertens, F. Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer. Nature Genet. 36, 331–334 (2004)
Article CAS Google Scholar - Mitelman, F., Johansson, B. & Mertens, F. The impact of translocations and gene fusions on cancer causation. Nature Rev. Cancer 7, 233–245 (2007)
Article CAS Google Scholar - Futreal, P. A. et al. A census of human cancer genes. Nature Rev. Cancer 4, 177–183 (2004)
Article CAS Google Scholar - Stratton, M. R., Campbell, P. J. & Futreal, P. A. The cancer genome. Nature 458, 719–724 (2009)
Article CAS ADS Google Scholar - Sawyers, C. L. Chronic myeloid leukemia. N. Engl. J. Med. 340, 1330–1340 (1999)
Article CAS Google Scholar - Tomlins, S. A. et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310, 644–648 (2005)
Article CAS ADS Google Scholar - Soda, M. et al. Identification of the transforming EML4_–_ALK fusion gene in non-small-cell lung cancer. Nature 448, 561–566 (2007)
Article CAS ADS Google Scholar - Höglund, M., Gisselsson, D., Sall, T. & Mitelman, F. Coping with complexity. multivariate analysis of tumor karyotypes. Cancer Genet. Cytogenet. 135, 103–109 (2002)
Article Google Scholar - Bignell, G. R. et al. Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome Res. 17, 1296–1303 (2007)
Article CAS Google Scholar - Volik, S. et al. End-sequence profiling: sequence-based analysis of aberrant genomes. Proc. Natl Acad. Sci. USA 100, 7696–7701 (2003)
Article ADS Google Scholar - Ruan, Y. et al. Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Res. 17, 828–838 (2007)
Article CAS Google Scholar - Greenman, C. et al. Patterns of somatic mutation in human cancer genomes. Nature 446, 153–158 (2007)
Article CAS ADS Google Scholar - Wood, L. D. et al. The genomic landscapes of human breast and colorectal cancers. Science 318, 1108–1113 (2007)
Article CAS ADS Google Scholar - The Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061–1068 (2008)
Article Google Scholar - Weir, B. A. et al. Characterizing the cancer genome in lung adenocarcinoma. Nature 450, 893–898 (2007)
Article CAS ADS Google Scholar - Campbell, P. J. et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nature Genet. 40, 722–729 (2008)
Article CAS Google Scholar - Weterings, E. & Chen, D. J. The endless tale of non-homologous end-joining. Cell Res. 18, 114–124 (2008)
Article CAS Google Scholar - van Gent, D. C. & van der Burg, M. Non-homologous end-joining, a sticky affair. Oncogene 26, 7731–7740 (2007)
Article CAS Google Scholar - Hefferin, M. L. & Tomkinson, A. E. Mechanism of DNA double-strand break repair by non-homologous end joining. DNA Repair 4, 639–648 (2005)
Article CAS Google Scholar - Hastings, P. J., Lupski, J. R., Rosenberg, S. M. & Ira, G. Mechanisms of change in gene copy number. Nature Rev. Genet. 10, 551–564 (2009)
Article CAS Google Scholar - Yan, C. T. et al. IgH class switching and translocations use a robust non-classical end-joining pathway. Nature 449, 478–482 (2007)
Article CAS ADS Google Scholar - Bohlander, S. K. ETV6: a versatile player in leukemogenesis. Semin. Cancer Biol. 15, 162–174 (2005)
Article CAS Google Scholar - Knezevich, S. R., McFadden, D. E., Tao, W., Lim, J. F. & Sorensen, P. H. A novel ETV6_–_NTRK3 gene fusion in congenital fibrosarcoma. Nature Genet. 18, 184–187 (1998)
Article CAS Google Scholar - Lannon, C. L. & Sorensen, P. H. ETV6–NTRK3: a chimeric protein tyrosine kinase with transformation activity in multiple cell lineages. Semin. Cancer Biol. 15, 215–223 (2005)
Article CAS Google Scholar - Jones, D. T. et al. Tandem duplication producing a novel oncogenic BRAF fusion gene defines the majority of pilocytic astrocytomas. Cancer Res. 68, 8673–8677 (2008)
Article CAS Google Scholar - Basecke, J., Whelan, J. T., Griesinger, F. & Bertrand, F. E. The MLL partial tandem duplication in acute myeloid leukaemia. Br. J. Haematol. 135, 438–449 (2006)
Article Google Scholar - Blow, J. J. & Gillespie, P. J. Replication licensing and cancer—a fatal entanglement? Nature Rev. Cancer 8, 799–806 (2008)
Article CAS Google Scholar - Perou, C. M. et al. Molecular portraits of human breast tumours. Nature 406, 747–752 (2000)
Article CAS ADS Google Scholar - Sorlie, T. et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl Acad. Sci. USA 98, 10869–10874 (2001)
Article CAS ADS Google Scholar - Chin, K. et al. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 10, 529–541 (2006)
Article CAS Google Scholar - Bergamaschi, A. et al. Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosom. Cancer 45, 1033–1040 (2006)
Article CAS Google Scholar - Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851–1858 (2008)
Article CAS Google Scholar - Ning, Z., Cox, A. J. & Mullikin, J. C. SSAHA: a fast search method for large DNA databases. Genome Res. 11, 1725–1729 (2001)
Article CAS Google Scholar - Venkatraman, E. & Olshen, A. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23, 657–663 (2007)
Article CAS Google Scholar - Lambros, M. et al. Unlocking pathology archives for molecular genetic studies: a reliable method to generate probes for chromogenic and fluorescent in situ hybridization. Lab. Invest. 86, 398–408 (2006)
Article CAS Google Scholar - Abeysinghe, S. S. et al. Translocation and gross deletion breakpoints in human inherited disease and cancer I: Nucleotide composition and recombination-associated motifs. Hum. Mutat. 22, 229–244 (2003)
Article CAS Google Scholar - Scholz, F. W. & Stephens, M. A. K-sample Anderson-Darling tests. Am. J. Stat. Assoc. 82, 918–924 (1987)
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Acknowledgements
We are grateful to M. Lambros, F. Geyer and R. Vatcheva for their assistance in the FISH experiments. We would like to acknowledge the support of the Kay Kendall Leukaemia Fund under Grant KKL282, Human Frontiers Award reference LT000561/2009-L, the Dana-Farber/Harvard SPORE in breast cancer under NCI grant reference CA089393, Breakthrough Breast Cancer, the Research Council of Norway Grants no. 155218 and 175240, and the Wellcome Trust under grant reference 077012/Z/05/Z.
Author Contributions M.R.S., P.A.F., P.J.C. and P.J.S. designed the experiment. S.E., D.J.M., P.J.S., M-L.L., I.V., L.J.M., J.B., M.A.Q., H.S., C.C., R.N., A.M.S., A.L., J.W.M.M. and C.Latimer carried out laboratory analyses. J.A.F., J.S.R.-F., L.v.V., A.L.R. D.P.S. and A.-L.B.-D. provided clinical samples. P.J.S., D.J.M., I.V., M.-L.L., E.D.P., J.T.S., L.A.S., C.Leroy, C.D.G., M.J., J.W.T., K.W.L., P.J.C., P.A.F., J.S.R.-F., J.W.M.M., A.M.S., J.A.F., M.R.S., H.E.G.R., A.L.R., A.-L.B.-D., L.v.V., A.L., P.J.C. and P.A.F. performed data analysis, informatics and statistics. M.R.S. wrote the manuscript with comments from P.J.S., P.A.F., P.J.C., A.-L.B.-D., J.S.R.-F., J.A.F., A.L.R., D.P.S. and L.v.V.
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Authors and Affiliations
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK ,
Philip J. Stephens, David J. McBride, Meng-Lay Lin, Ignacio Varela, Erin D. Pleasance, Jared T. Simpson, Lucy A. Stebbings, Catherine Leroy, Sarah Edkins, Laura J. Mudie, Chris D. Greenman, Mingming Jia, Calli Latimer, Jon W. Teague, King Wai Lau, John Burton, Michael A. Quail, Harold Swerdlow, Carol Churcher, Peter J. Campbell, P. Andrew Futreal & Michael R. Stratton - Molecular Pathology Laboratory, The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK ,
Rachael Natrajan & Jorge S. Reis-Filho - Department of Medical Oncology, Josephine Nefkens Institute, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands,
Anieta M. Sieuwerts, John W. M. Martens & John A. Foekens - Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA,
Daniel P. Silver & Andrea L. Richardson - Department of Genetics, Norwegian Radium Hospital, Oslo University Hospital, Montebello, N-0310 Oslo, Norway,
Anita Langerød, Hege E. G. Russnes & Anne-Lise Børresen-Dale - The Netherlands Cancer Institute, 121 Plesmanlaan, 1066 CX Amsterdam, The Netherlands ,
Laura van ’t Veer - Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA,
Andrea L. Richardson - Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Montebello, 0310 Oslo, Norway,
Anne-Lise Børresen-Dale - Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK. ,
Michael R. Stratton
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Stephens, P., McBride, D., Lin, ML. et al. Complex landscapes of somatic rearrangement in human breast cancer genomes.Nature 462, 1005–1010 (2009). https://doi.org/10.1038/nature08645
- Received: 20 July 2009
- Accepted: 05 November 2009
- Issue Date: 24 December 2009
- DOI: https://doi.org/10.1038/nature08645