Integrated genomic analyses of ovarian carcinoma
Bell, D.; Berchuck, A.; Birrer, M.; Chien, J.; Cramer, D. W.; Dao, F.; Dhir, R.; DiSaia, P.; Gabra, H.; Glenn, P.; Godwin, A. K.; Gross, J.; Hartmann, L.; Huang, M.; Huntsman, D. G.; Iacocca, M.; Imielinski, M.; Kalloger, S.; Karlan, B. Y.; Levine, D. A.; Mills, G. B.; Morrison, C.; Mutch, D.; Olvera, N.; Orsulic, S.; Park, K.; Petrelli, N.; Rabeno, B.; Rader, J. S.; Sikic, B. I.; Smith-McCune, K.; Sood, A. K.; Bowtell, D.; Penny, R.; Testa, J. R.; Chang, K.; Dinh, H. H.; Drummond, J. A.; Fowler, G.; Gunaratne, P.; Hawes, A. C.; Kovar, C. L.; Lewis, L. R.; Morgan, M. B.; Newsham, I. F.; Santibanez, J.; Reid, J. G.; Trevino, L. R.; Wu, Y.-Q.; Wang, M.; Muzny, D. M.; Wheeler, D. A.; Gibbs, R. A.; Getz, G.; Lawrence, M. S.; Cibulskis, K.; Sivachenko, A. Y.; Sougnez, C.; Voet, D.; Wilkinson, J.; Bloom, T.; Ardlie, K.; Fennell, T.; Baldwin, J.; Gabriel, S.; Lander, E. S.; Ding, L.; Fulton, R. S.; Koboldt, D. C.; McLellan, M. D.; Wylie, T.; Walker, J.; Oâ Laughlin, M.; Dooling, D. J.; Fulton, L.; Abbott, R.; Dees, N. D.; Zhang, Q.; Kandoth, C.; Wendl, M.; Schierding, W.; Shen, D.; Harris, C. C.; Schmidt, H.; Kalicki, J.; Delehaunty, K. D.; Fronick, C. C.; Demeter, R.; Cook, L.; Wallis, J. W.; Lin, L.; Magrini, V. J.; Hodges, J. S.; Eldred, J. M.; Smith, S. M.; Pohl, C. S.; Vandin, F.; Raphael, B. J.; Weinstock, G. M.; Mardis, E. R.; Wilson, R. K.; Meyerson, M.; Winckler, W.; Getz, G.; Verhaak, R. G. W.; Carter, S. L.; Mermel, C. H.; Saksena, G.; Nguyen, H.; Onofrio, R. C.; Lawrence, M. S.; Hubbard, D.; Gupta, S.; Crenshaw, A.; Ramos, A. H.; Ardlie, K.; Chin, L.; Protopopov, A.; Zhang, Juinhua; Kim, T. M.; Perna, I.; Xiao, Y.; Zhang, H.; Ren, G.; Sathiamoorthy, N.; Park, R. W.; Lee, E.; Park, P. J.; Kucherlapati, R.; Absher, D. M.; Waite, L.; Sherlock, G.; Brooks, J. D.; Li, J. Z.; Xu, J.; Myers, R. M.; Laird, P. W.; Cope, L.; Herman, J. G.; Shen, H.; Weisenberger, D. J.; Noushmehr, H.; Pan, F.; Triche Jr, T.; Berman, B. P.; Van Den Berg, D. J.; Buckley, J.; Baylin, S. B.; Spellman, P. T.; Purdom, E.; Neuvial, P.; Bengtsson, H.; Jakkula, L. R.; Durinck, S.; Han, J.; Dorton, S.; Marr, H.; Choi, Y. G.; Wang, V.; Wang, N. J.; Ngai, J.; Conboy, J. G.; Parvin, B.; Feiler, H. S.; Speed, T. P.; Gray, J. W.; Levine, D. A.; Socci, N. D.; Liang, Y.; Taylor, B. S.; Schultz, N.; Borsu, L.; Lash, A. E.; Brennan, C.; Viale, A.; Sander, C.; Ladanyi, M.; Hoadley, K. A.; Meng, S.; Du, Y.; Shi, Y.; Li, L.; Turman, Y. J.; Zang, D.; Helms, E. B.; Balu, S.; Zhou, X.; Wu, J.; Topal, M. D.; Hayes, D. N.; Perou, C. M.; Getz, G.; Voet, D.; Saksena, G.; Zhang, Junihua; Zhang, H.; Wu, C. J.; Shukla, S.; Cibulskis, K.; Lawrence, M. S.; Sivachenko, A.; Jing, R.; Park, R. W.; Liu, Y.; Park, P. J.; Noble, M.; Chin, L.; Carter, H.; Kim, D.; Karchin, R.; Spellman, P. T.; Purdom, E.; Neuvial, P.; Bengtsson, H.; Durinck, S.; Han, J.; Korkola, J. E.; Heiser, L. M.; Cho, R. J.; Hu, Z.; Parvin, B.; Speed, T. P.; Gray, J. W.; Schultz, N.; Cerami, E.; Taylor, B. S.; Olshen, A.; Reva, B.; Antipin, Y.; Shen, R.; Mankoo, P.; Sheridan, R.; Ciriello, G.; Chang, W. K.; Bernanke, J. A.; Borsu, L.; Levine, D. A.; Ladanyi, M.; Sander, C.; Haussler, D.; Benz, C. C.; Stuart, J. M.; Benz, S. C.; Sanborn, J. Z.; Vaske, C. J.; Zhu, J.; Szeto, C.; Scott, G. K.; Yau, C.; Hoadley, K. A.; Du, Y.; Balu, S.; Hayes, D. N.; Perou, C. M.; Wilkerson, M. D.; Zhang, N.; Akbani, R.; Baggerly, K. A.; Yung, W. K.; Mills, G. B.; Weinstein, J. N.; Penny, R.; Shelton, T.; Grimm, D.; Hatfield, M.; Morris, S.; Yena, P.; Rhodes, P.; Sherman, M.; Paulauskis, J.; Millis, S.; Kahn, A.; Greene, J. M.; Sfeir, R.; Jensen, M. A.; Chen, J.; Whitmore, J.; Alonso, S.; Jordan, J.; Chu, A.; Zhang, Jinghui; Barker, A.; Compton, C.; Eley, G.; Ferguson, M.; Fielding, P.; Gerhard, D. S.; Myles, R.; Schaefer, C.; Mills Shaw, K. R.; Vaught, J.; Vockley, J. B.; Good, P. J.; Guyer, M. S.; Ozenberger, B.; Peterson, J.; Thomson, E.; The Cancer Genome Atlas Research Network; (Participants are arranged by area of contribution and then by institution.); Disease working group and tissue source sites; Genome sequencing centres: Baylor College of Medicine; Broad Institute; Washington University in St Louis; Cancer genome characterization centres: Broad Institute/Dana-Farber Cancer Institute; Harvard Medical School; HudsonAlpha Institute/Stanford University; University of Southern California/Johns Hopkins University; Lawrence Berkeley National Laboratory; Memorial Sloan-Kettering Cancer Center; University of North Carolina at Chapel Hill; Genome data analysis centres: Broad Institute; Johns Hopkins University; Lawrence Berkeley National Laboratory; Memorial Sloan-Kettering Cancer Center; University of California Santa Cruz/Buck Institute; University of North Carolina at Chapel Hill; The University of Texas MD Anderson Cancer Center; Biospecimen core resource; Data coordination centre; Project teams: National Cancer Institute; National Human Genome Research Institute; Bell, D.; Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.; Berchuck, A.; Division of Gynecologic Oncology/Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina 27708, USA.; Duke Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, North Carolina 27708, USA.; Birrer, M.; Department of Medicine, Harvard Medical School, Boston, Massachusetts 02114, USA.; Gynecologic Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.; Chien, J.; Division of Experimental Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.; Cramer, D. W.; Department of Obstetrics and Gynecology Epidemiology Center, Brigham and Womenâ s Hospital, Boston, Massachusetts 02115, USA.; Dao, F.; Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.; Dhir, R.; Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.; DiSaia, P.; Gynecologic Oncology Group, University of California Irvine, Irvine, California 92697, USA.; Gabra, H.; Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London Hammersmith Campus, London W12 0NN, UK.; Glenn, P.; Department of Obstetrics, Gynecology and Reproductive Services, University of California San Francisco, San Francisco, California 94143, USA.; Godwin, A. K.; Womenâ s Cancer Program, Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA.; Gross, J.; Womenâ s Cancer Research Institute at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Geffen School of Medicine at UCLA, Los Angeles, California 90048, USA.; Hartmann, L.; Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota 55905, USA.; Huang, M.; Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA.; Huntsman, D. G.; Center for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1G1, Canada.; Iacocca, M.; Department of Pathology, Christiana Care Health Services, Newark, Delaware 19718, USA.; Imielinski, M.; Gynecologic Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.; Kalloger, S.; Center for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1G1, Canada.; Karlan, B. Y.; Womenâ s Cancer Research Institute at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Geffen School of Medicine at UCLA, Los Angeles, California 90048, USA.; Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Geffen School of Medicine at UCLA, Los Angeles, California 90048, USA.; Levine, D. A.; Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.; Mills, G. B.; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.; Kleberg Center for Molecular Markers, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.; Morrison, C.; The Department of Pathology and Laboratory Medicine, Roswell Park Cancer Institute, Buffalo, New York 14263, USA.; Division of Molecular Pathology, Roswell Park Cancer Institute, Buffalo, New York 14263, USA.; Mutch, D.; Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Washington University School of Medicine in St Louis, St Louis, Missouri 63110, USA.; Olvera, N.; Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.; Orsulic, S.; Womenâ s Cancer Research Institute at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Geffen School of Medicine at UCLA, Los Angeles, California 90048, USA.; Park, K.; Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.; Petrelli, N.; Department of Surgery, Helen F Graham Cancer Center at Christina Care, Newark, Delaware 19713, USA.; Rabeno, B.; Department of Pathology, Christiana Care Health Services, Newark, Delaware 19718, USA.; Rader, J. S.; Department of Obstetrics and Gynecology, Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.; Sikic, B. I.; Division of Oncology, Department of Medicine, Stanford University School of Medicine, Palo Alto, California 94304, USA.; Smith-McCune, K.; Department of Obstetrics, Gynecology and Reproductive Services, University of California San Francisco, San Francisco, California 94143, USA.; Sood, A. K.; Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77230, USA.; Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas 77230, USA.; Bowtell, D.; Research Division, Peter MacCallum Cancer Centre, Locked Bag 1, Aâ Beckett St, Melbourne, Victoria 8006, Australia.; Penny, R.; International Genomics Consortium, Phoenix, Arizona 85004, USA.; Testa, J. R.; Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA.; Chang, K.; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.; Dinh, H. H.; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.; Drummond, J. A.; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.; Fowler, G.; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.; Gunaratne, P.; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.; Hawes, A. C.; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.; Kovar, C. L.; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.; Lewis, L. R.; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.; Morgan, M. B.; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.; Newsham, I. F.; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.; Santibanez, J.; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.; Reid, J. G.; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.; Trevino, L. R.; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.; Wu, Y.-Q.; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.; Wang, M.; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.; Muzny, D. M.; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.; Wheeler, D. A.; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.; Gibbs, R. A.; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.; Getz, G.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Lawrence, M. S.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Cibulskis, K.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Medical Sequencing Analysis and Informatics, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Sivachenko, A. Y.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Sougnez, C.; Cancer Genome & Medical Resequencing Projects, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Voet, D.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Wilkinson, J.; Sequencing Platform, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Bloom, T.; Sequencing Platform Informatics, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Ardlie, K.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Fennell, T.; Directed Sequencing Informatics, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Baldwin, J.; Sequencing Platform, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Gabriel, S.; Genetic Analysis Platform, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Lander, E. S.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.; Department of Systems Biology, Harvard University, Boston, Massachusetts 02115, USA.; Ding, L.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Fulton, R. S.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Koboldt, D. C.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; McLellan, M. D.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Wylie, T.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Walker, J.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Oâ Laughlin, M.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Dooling, D. J.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Fulton, L.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Abbott, R.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Dees, N. D.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Zhang, Q.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Kandoth, C.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Wendl, M.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Schierding, W.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Shen, D.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Harris, C. C.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Schmidt, H.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Kalicki, J.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Delehaunty, K. D.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Fronick, C. C.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Demeter, R.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Cook, L.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Wallis, J. W.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Lin, L.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Magrini, V. J.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Hodges, J. S.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Eldred, J. M.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Smith, S. M.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Pohl, C. S.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Vandin, F.; Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912, USA.; Raphael, B. J.; Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912, USA.; Weinstock, G. M.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Mardis, E. R.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Wilson, R. K.; The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri 63108, USA.; Meyerson, M.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.; Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA; Winckler, W.; Cancer Genome & Medical Resequencing Projects, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Getz, G.; Cancer Genome & Medical Resequencing Projects, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Verhaak, R. G. W.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.; Carter, S. L.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.; Mermel, C. H.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.; Saksena, G.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Nguyen, H.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Onofrio, R. C.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Lawrence, M. S.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Hubbard, D.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.; Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA; Gupta, S.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Crenshaw, A.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Ramos, A. H.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.; Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA; Ardlie, K.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Chin, L.; Belfer Institute for Applied Cancer Science, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.; Department of Dermatology, Harvard Medical School, Boston, Massachusetts 02115, USA.; Protopopov, A.; Belfer Institute for Applied Cancer Science, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.; Zhang, Juinhua; Belfer Institute for Applied Cancer Science, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.; Kim, T. M.; The Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.; Perna, I.; Belfer Institute for Applied Cancer Science, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.; Xiao, Y.; Belfer Institute for Applied Cancer Science, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.; Zhang, H.; Belfer Institute for Applied Cancer Science, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.; Ren, G.; Belfer Institute for Applied Cancer Science, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.; Sathiamoorthy, N.; Partners Center for Personalized Genetic Medicine, Cambridge, Massachusetts 02139, USA.; Park, R. W.; The Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.; Lee, E.; The Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.; Park, P. J.; The Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.; Informatics Program, Childrenâ s Hospital, Boston, Massachusetts 02115, USA.; Kucherlapati, R.; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.; Absher, D. M.; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA.; Waite, L.; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA.; Sherlock, G.; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.; Brooks, J. D.; Department of Urology, Stanford University School of Medicine, Stanford, California 94305, USA.; Li, J. Z.; Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA.; Xu, J.; Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA.; Myers, R. M.; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA.; Laird, P. W.; University of Southern California Epigenome Center, University of Southern California, Los Angeles, California 90089, USA.; Cope, L.; Biometry and Clinical Trials Division, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Maryland 21231, USA.; Herman, J. G.; Cancer Biology Division, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Maryland 21231, USA.; Shen, H.; University of Southern California Epigenome Center, University of Southern California, Los Angeles, California 90089, USA.; Weisenberger, D. J.; University of Southern California Epigenome Center, University of Southern California, Los Angeles, California 90089, USA.; Noushmehr, H.; University of Southern California Epigenome Center, University of Southern California, Los Angeles, California 90089, USA.; Pan, F.; University of Southern California Epigenome Center, University of Southern California, Los Angeles, California 90089, USA.; Triche Jr, T.; University of Southern California Epigenome Center, University of Southern California, Los Angeles, California 90089, USA.; Berman, B. P.; University of Southern California Epigenome Center, University of Southern California, Los Angeles, California 90089, USA.; Van Den Berg, D. J.; University of Southern California Epigenome Center, University of Southern California, Los Angeles, California 90089, USA.; Buckley, J.; University of Southern California Epigenome Center, University of Southern California, Los Angeles, California 90089, USA.; Baylin, S. B.; Cancer Biology Division, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Maryland 21231, USA.; Spellman, P. T.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Purdom, E.; Department of Statistics, University of California at Berkeley, Berkeley, California 95720, USA.; Neuvial, P.; Department of Statistics, University of California at Berkeley, Berkeley, California 95720, USA.; Bengtsson, H.; Department of Statistics, University of California at Berkeley, Berkeley, California 95720, USA.; Jakkula, L. R.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Durinck, S.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Han, J.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Dorton, S.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Marr, H.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Choi, Y. G.; Department of Molecular and Cellular Biology, University of California at Berkeley, Berkeley, California 95720, USA.; Wang, V.; Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004, USA.; Wang, N. J.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Ngai, J.; Department of Molecular and Cellular Biology, University of California at Berkeley, Berkeley, California 95720, USA.; Conboy, J. G.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Parvin, B.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Feiler, H. S.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Speed, T. P.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Walter and Eliza Hall Institute, Parkville, Victoria 3052, Australia.; Gray, J. W.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Levine, D. A.; Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.; Socci, N. D.; Computational Biology Center, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Liang, Y.; Computational Biology Center, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Taylor, B. S.; Computational Biology Center, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Schultz, N.; Computational Biology Center, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Borsu, L.; Department of Pathology, Human Oncology and Pathogenesis Program, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Lash, A. E.; Computational Biology Center, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Brennan, C.; Department of Neurosurgery, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Viale, A.; Genomics Core Laboratory, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Sander, C.; Computational Biology Center, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Ladanyi, M.; Department of Pathology, Human Oncology and Pathogenesis Program, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Hoadley, K. A.; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.; Department of Pathology and Laboratory Medicine, Chapel Hill, North Carolina 27599, USA.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Meng, S.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Du, Y.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Shi, Y.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Li, L.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Turman, Y. J.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Zang, D.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Helms, E. B.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Balu, S.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Zhou, X.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Wu, J.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Topal, M. D.; Department of Pathology and Laboratory Medicine, Chapel Hill, North Carolina 27599, USA.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Hayes, D. N.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Department of Internal Medicine, Division of Medical Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.; Perou, C. M.; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.; Department of Pathology and Laboratory Medicine, Chapel Hill, North Carolina 27599, USA.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Getz, G.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Voet, D.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Saksena, G.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Zhang, Junihua; Belfer Institute for Applied Cancer Science, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.; Zhang, H.; Belfer Institute for Applied Cancer Science, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.; Wu, C. J.; Belfer Institute for Applied Cancer Science, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.; Shukla, S.; Belfer Institute for Applied Cancer Science, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.; Cibulskis, K.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Medical Sequencing Analysis and Informatics, The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Lawrence, M. S.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Sivachenko, A.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Jing, R.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Park, R. W.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; The Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.; Liu, Y.; Belfer Institute for Applied Cancer Science, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.; Park, P. J.; The Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.; Informatics Program, Childrenâ s Hospital, Boston, Massachusetts 02115, USA.; Noble, M.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Chin, L.; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA.; Belfer Institute for Applied Cancer Science, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.; Department of Dermatology, Harvard Medical School, Boston, Massachusetts 02115, USA.; Carter, H.; Institute for Computational Medicine, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21231, USA; Kim, D.; Institute for Computational Medicine, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21231, USA; Karchin, R.; Institute for Computational Medicine, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21231, USA; Spellman, P. T.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Purdom, E.; Department of Statistics, University of California at Berkeley, Berkeley, California 95720, USA.; Neuvial, P.; Department of Statistics, University of California at Berkeley, Berkeley, California 95720, USA.; Bengtsson, H.; Department of Statistics, University of California at Berkeley, Berkeley, California 95720, USA.; Durinck, S.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Han, J.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Korkola, J. E.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Heiser, L. M.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Cho, R. J.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Hu, Z.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Parvin, B.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Speed, T. P.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Walter and Eliza Hall Institute, Parkville, Victoria 3052, Australia.; Gray, J. W.; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.; Schultz, N.; Computational Biology Center, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Cerami, E.; Computational Biology Center, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Taylor, B. S.; Computational Biology Center, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Olshen, A.; Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.; Reva, B.; Computational Biology Center, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Antipin, Y.; Computational Biology Center, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Shen, R.; Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.; Mankoo, P.; Computational Biology Center, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Sheridan, R.; Computational Biology Center, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Ciriello, G.; Computational Biology Center, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Chang, W. K.; Computational Biology Center, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Department of Physiology and Biophysics, Weill Cornell Graduate School of Medical Sciences, New York, New York 10065, USA.; Bernanke, J. A.; Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, USA.; Borsu, L.; Department of Pathology, Human Oncology and Pathogenesis Program, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Levine, D. A.; Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.; Ladanyi, M.; Department of Pathology, Human Oncology and Pathogenesis Program, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Sander, C.; Computational Biology Center, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.; Haussler, D.; Department of Biomolecular Engineering and Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA.; Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California 95064, USA.; Benz, C. C.; Buck Institute for Age Research, Novato, California 94945, USA.; Stuart, J. M.; Department of Biomolecular Engineering and Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA.; Benz, S. C.; Department of Biomolecular Engineering and Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA.; Sanborn, J. Z.; Department of Biomolecular Engineering and Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA.; Vaske, C. J.; Department of Biomolecular Engineering and Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA.; Lewis-Sigler Institute for Integrative Genomics, Princeton, New Jersey 08544, USA.; Zhu, J.; Department of Biomolecular Engineering and Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA.; Szeto, C.; Department of Biomolecular Engineering and Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA.; Scott, G. K.; Buck Institute for Age Research, Novato, California 94945, USA.; Yau, C.; Buck Institute for Age Research, Novato, California 94945, USA.; Hoadley, K. A.; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.; Department of Pathology and Laboratory Medicine, Chapel Hill, North Carolina 27599, USA.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Du, Y.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Balu, S.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Hayes, D. N.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Department of Internal Medicine, Division of Medical Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.; Perou, C. M.; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.; Department of Pathology and Laboratory Medicine, Chapel Hill, North Carolina 27599, USA.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Wilkerson, M. D.; Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA.; Zhang, N.; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.; Akbani, R.; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.; Baggerly, K. A.; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.; Yung, W. K.; Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.; Mills, G. B.; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.; Kleberg Center for Molecular Markers, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.; Weinstein, J. N.; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.; Penny, R.; International Genomics Consortium, Phoenix, Arizona 85004, USA.; Shelton, T.; International Genomics Consortium, Phoenix, Arizona 85004, USA.; Grimm, D.; International Genomics Consortium, Phoenix, Arizona 85004, USA.; Hatfield, M.; International Genomics Consortium, Phoenix, Arizona 85004, USA.; Morris, S.; International Genomics Consortium, Phoenix, Arizona 85004, USA.; Yena, P.; International Genomics Consortium, Phoenix, Arizona 85004, USA.; Rhodes, P.; International Genomics Consortium, Phoenix, Arizona 85004, USA.; Sherman, M.; International Genomics Consortium, Phoenix, Arizona 85004, USA.; Paulauskis, J.; International Genomics Consortium, Phoenix, Arizona 85004, USA.; Millis, S.; International Genomics Consortium, Phoenix, Arizona 85004, USA.; Kahn, A.; SRA International, Fairfax, Virginia 22033, USA.; Greene, J. M.; SRA International, Fairfax, Virginia 22033, USA.; Sfeir, R.; SRA International, Fairfax, Virginia 22033, USA.; Jensen, M. A.; SRA International, Fairfax, Virginia 22033, USA.; Chen, J.; SRA International, Fairfax, Virginia 22033, USA.; Whitmore, J.; SRA International, Fairfax, Virginia 22033, USA.; Alonso, S.; SRA International, Fairfax, Virginia 22033, USA.; Jordan, J.; SRA International, Fairfax, Virginia 22033, USA.; Chu, A.; SRA International, Fairfax, Virginia 22033, USA.; Zhang, Jinghui; Department of Biotechnology, St Jude Childrenâ s Research Hospital, Memphis, Tennessee 38105, USA.; Barker, A.; Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.; Compton, C.; Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.; Eley, G.; Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.; Ferguson, M.; MLF Consulting, Arlington, Massachusetts 02474, USA.; Fielding, P.; Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.; Gerhard, D. S.; Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.; Myles, R.; Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.; Schaefer, C.; Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.; Mills Shaw, K. R.; Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.; Vaught, J.; Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.; Vockley, J. B.; Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.; Good, P. J.; National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.; Guyer, M. S.; National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.; Ozenberger, B.; National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.; Peterson, J.; National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.; Thomson, E.; National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
Журнал:
Nature
Дата:
2011
Аннотация:
A catalogue of molecular aberrations that cause ovarian cancer is critical for developing and deploying therapies that will improve patientsâ lives. The Cancer Genome Atlas project has analysed messenger RNA expression, microRNA expression, promoter methylation and DNA copy number in 489 high-grade serous ovarian adenocarcinomas and the DNA sequences of exons from coding genes in 316 of these tumours. Here we report that high-grade serous ovarian cancer is characterized by TP53 mutations in almost all tumours (96%); low prevalence but statistically recurrent somatic mutations in nine further genes including NF1, BRCA1, BRCA2, RB1 and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes. Analyses delineated four ovarian cancer transcriptional subtypes, three microRNA subtypes, four promoter methylation subtypes and a transcriptional signature associated with survival duration, and shed new light on the impact that tumours with BRCA1/2 (BRCA1 or BRCA2) and CCNE1 aberrations have on survival. Pathway analyses suggested that homologous recombination is defective in about half of the tumours analysed, and that NOTCH and FOXM1 signalling are involved in serous ovarian cancer pathophysiology.
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W.; ;; Beroukhim, Rameen; ;; Weir, Barbara A.; ;; Garraway, Levi; ;; Golub, Todd; ;; Meyerson, Matthew; ;; Chin, Lynda; ;; Kohane, Isaac S.; ;; Park, Peter J.; ; (Macmillan Publishers Limited. All rights reserved, 2008)
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Hudson (Chairperson), Thomas J.; Anderson, Warwick; Aretz, Axel; Barker, Anna D.; Bell, Cindy; Bernabé, Rosa R.; Bhan, M. K.; Calvo, Fabien; Eerola, Iiro; Gerhard, Daniela S.; Guttmacher, Alan; Guyer, Mark; Hemsley, Fiona M.; Jennings, Jennifer L.; Kerr, David; Klatt, Peter; Kolar, Patrik; Kusuda, Jun; Lane, David P.; Laplace, Frank; Lu, Youyong; Nettekoven, Gerd; Ozenberger, Brad; Peterson, Jane; Rao, T.S.; Remacle, Jacques; Schafer, Alan J.; Shibata, Tatsuhiro; Stratton, Michael R.; Vockley, Joseph G.; Watanabe, Koichi; Yang, Huanming; Yuen, Matthew M. F.; Knoppers (Leader), Bartha M.; Bobrow, Martin; Cambon-Thomsen, Anne; Dressler, Lynn G.; Dyke, Stephanie O. 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S.; Bhan, M. K.; Scarpa (Leader), Aldo; Pederzoli, Paolo; Lawlor, Rita T.; Delledonne, Massimo; Bardelli, Alberto; Biankin, Andrew V.; Grimmond, Sean M.; Gress, Thomas; Klimstra, David; Zamboni, Giuseppe; Shibata (Leader), Tatsuhiro; Nakamura, Yusuke; Nakagawa, Hidewaki; Kusuda, Jun; Tsunoda, Tatsuhiko; Miyano, Satoru; Aburatani, Hiroyuki; Kato, Kazuto; Fujimoto, Akihiro; Yoshida, Teruhiko; Campo (Leader), Elias; López-OtÃn, Carlos; Estivill, Xavier; Guigó, Roderic; de Sanjosé, Silvia; Piris, Miguel A.; Montserrat, Emili; González-DÃaz, Marcos; Puente, Xose S.; Jares, Pedro; Valencia, Alfonso; Himmelbaue, Heinz; Quesada, Victor; Bea, Silvia; Stratton (Leader), Michael R.; Futreal, P. 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