The sequence and de novo assembly of the giant panda genome
Li, Ruiqiang; Fan, Wei; Tian, Geng; Zhu, Hongmei; He, Lin; Cai, Jing; Huang, Quanfei; Cai, Qingle; Li, Bo; Bai, Yinqi; Zhang, Zhihe; Zhang, Yaping; Wang, Wen; Li, Jun; Wei, Fuwen; Li, Heng; Jian, Min; Li, Jianwen; Zhang, Zhaolei; Nielsen, Rasmus; Li, Dawei; Gu, Wanjun; Yang, Zhentao; Xuan, Zhaoling; Ryder, Oliver A.; Leung, Frederick Chi-Ching; Zhou, Yan; Cao, Jianjun; Sun, Xiao; Fu, Yonggui; Fang, Xiaodong; Guo, Xiaosen; Wang, Bo; Hou, Rong; Shen, Fujun; Mu, Bo; Ni, Peixiang; Lin, Runmao; Qian, Wubin; Wang, Guodong; Yu, Chang; Nie, Wenhui; Wang, Jinhuan; Wu, Zhigang; Liang, Huiqing; Min, Jiumeng; Wu, Qi; Cheng, Shifeng; Ruan, Jue; Wang, Mingwei; Shi, Zhongbin; Wen, Ming; Liu, Binghang; Ren, Xiaoli; Zheng, Huisong; Dong, Dong; Cook, Kathleen; Shan, Gao; Zhang, Hao; Kosiol, Carolin; Xie, Xueying; Lu, Zuhong; Zheng, Hancheng; Li, Yingrui; Steiner, Cynthia C.; Lam, Tommy Tsan-Yuk; Lin, Siyuan; Zhang, Qinghui; Li, Guoqing; Tian, Jing; Gong, Timing; Liu, Hongde; Zhang, Dejin; Fang, Lin; Ye, Chen; Zhang, Juanbin; Hu, Wenbo; Xu, Anlong; Ren, Yuanyuan; Zhang, Guojie; Bruford, Michael W.; Li, Qibin; Ma, Lijia; Guo, Yiran; An, Na; Hu, Yujie; Zheng, Yang; Shi, Yongyong; Li, Zhiqiang; Liu, Qing; Chen, Yanling; Zhao, Jing; Qu, Ning; Zhao, Shancen; Tian, Feng; Wang, Xiaoling; Wang, Haiyin; Xu, Lizhi; Liu, Xiao; Vinar, Tomas; Wang, Yajun; Lam, Tak-Wah; Yiu, Siu-Ming; Liu, Shiping; Zhang, Hemin; Li, Desheng; Huang, Yan; Wang, Xia; Yang, Guohua; Jiang, Zhi; Wang, Junyi; Qin, Nan; Li, Li; Li, Jingxiang; Bolund, Lars; Kristiansen, Karsten; Wong, Gane Ka-Shu; Olson, Maynard; Zhang, Xiuqing; Li, Songgang; Yang, Huanming; Wang, Jian; Wang, Jun; Li, Ruiqiang; BGI-Shenzhen, Shenzhen 518083, China; Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark; Fan, Wei; BGI-Shenzhen, Shenzhen 518083, China; Tian, Geng; BGI-Shenzhen, Shenzhen 518083, China; The Graduate University of Chinese Academy of Sciences, Beijing 100062, China; Zhu, Hongmei; BGI-Shenzhen, Shenzhen 518083, China; He, Lin; Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China; Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China; Cai, Jing; The Graduate University of Chinese Academy of Sciences, Beijing 100062, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Huang, Quanfei; BGI-Shenzhen, Shenzhen 518083, China; Cai, Qingle; BGI-Shenzhen, Shenzhen 518083, China; Genome Research Institute, Shenzhen University Medical School, Shenzhen 518000, China; Li, Bo; BGI-Shenzhen, Shenzhen 518083, China; Bai, Yinqi; BGI-Shenzhen, Shenzhen 518083, China; Zhang, Zhihe; Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; Zhang, Yaping; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Wang, Wen; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Li, Jun; BGI-Shenzhen, Shenzhen 518083, China; Wei, Fuwen; Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, the Chinese Academy of Sciences, Beichenxilu 1-5, Chaoyang District, Beijing 100101, China; Li, Heng; Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Jian, Min; BGI-Shenzhen, Shenzhen 518083, China; Li, Jianwen; BGI-Shenzhen, Shenzhen 518083, China; Zhang, Zhaolei; Banting and Best Department of Medical Research, Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada; Nielsen, Rasmus; Departments of Integrative Biology and Statistics, UC-Berkeley, 3060 VLSB, Berkeley, California 94720, USA; Li, Dawei; BGI-Shenzhen, Shenzhen 518083, China; Gu, Wanjun; Key Laboratory of Child Development and Learning Science, Southeast University, Ministry of Education, Nanjing 210096, China; Yang, Zhentao; BGI-Shenzhen, Shenzhen 518083, China; Xuan, Zhaoling; BGI-Shenzhen, Shenzhen 518083, China; Ryder, Oliver A.; San Diego Zooâ s Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, California 92027, USA; Leung, Frederick Chi-Ching; School of Biological Sciences, The University of Hong Kong, Hong Kong, China; Zhou, Yan; BGI-Shenzhen, Shenzhen 518083, China; Cao, Jianjun; BGI-Shenzhen, Shenzhen 518083, China; Sun, Xiao; State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China; Fu, Yonggui; State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, 510275 Guanghou, China; Fang, Xiaodong; BGI-Shenzhen, Shenzhen 518083, China; Guo, Xiaosen; BGI-Shenzhen, Shenzhen 518083, China; Wang, Bo; BGI-Shenzhen, Shenzhen 518083, China; Hou, Rong; Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; Shen, Fujun; Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; Mu, Bo; BGI-Shenzhen, Shenzhen 518083, China; Ni, Peixiang; BGI-Shenzhen, Shenzhen 518083, China; Lin, Runmao; BGI-Shenzhen, Shenzhen 518083, China; Qian, Wubin; BGI-Shenzhen, Shenzhen 518083, China; Wang, Guodong; The Graduate University of Chinese Academy of Sciences, Beijing 100062, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Yu, Chang; BGI-Shenzhen, Shenzhen 518083, China; Nie, Wenhui; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Wang, Jinhuan; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Wu, Zhigang; BGI-Shenzhen, Shenzhen 518083, China; Liang, Huiqing; BGI-Shenzhen, Shenzhen 518083, China; Min, Jiumeng; BGI-Shenzhen, Shenzhen 518083, China; Genome Research Institute, Shenzhen University Medical School, Shenzhen 518000, China; Wu, Qi; Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, the Chinese Academy of Sciences, Beichenxilu 1-5, Chaoyang District, Beijing 100101, China; Cheng, Shifeng; BGI-Shenzhen, Shenzhen 518083, China; Genome Research Institute, Shenzhen University Medical School, Shenzhen 518000, China; Ruan, Jue; BGI-Shenzhen, Shenzhen 518083, China; The Graduate University of Chinese Academy of Sciences, Beijing 100062, China; Wang, Mingwei; BGI-Shenzhen, Shenzhen 518083, China; Shi, Zhongbin; BGI-Shenzhen, Shenzhen 518083, China; Wen, Ming; BGI-Shenzhen, Shenzhen 518083, China; Liu, Binghang; BGI-Shenzhen, Shenzhen 518083, China; Ren, Xiaoli; BGI-Shenzhen, Shenzhen 518083, China; Zheng, Huisong; BGI-Shenzhen, Shenzhen 518083, China; Dong, Dong; Banting and Best Department of Medical Research, Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada; Cook, Kathleen; Banting and Best Department of Medical Research, Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada; Shan, Gao; BGI-Shenzhen, Shenzhen 518083, China; Zhang, Hao; BGI-Shenzhen, Shenzhen 518083, China; Kosiol, Carolin; Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Veterinärplatz 1, 1210 Wien, Austria; Xie, Xueying; Key Laboratory of Child Development and Learning Science, Southeast University, Ministry of Education, Nanjing 210096, China; Lu, Zuhong; Key Laboratory of Child Development and Learning Science, Southeast University, Ministry of Education, Nanjing 210096, China; Zheng, Hancheng; BGI-Shenzhen, Shenzhen 518083, China; Li, Yingrui; BGI-Shenzhen, Shenzhen 518083, China; The Graduate University of Chinese Academy of Sciences, Beijing 100062, China; Steiner, Cynthia C.; San Diego Zooâ s Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, California 92027, USA; Lam, Tommy Tsan-Yuk; School of Biological Sciences, The University of Hong Kong, Hong Kong, China; Lin, Siyuan; BGI-Shenzhen, Shenzhen 518083, China; Zhang, Qinghui; BGI-Shenzhen, Shenzhen 518083, China; Li, Guoqing; BGI-Shenzhen, Shenzhen 518083, China; Tian, Jing; BGI-Shenzhen, Shenzhen 518083, China; Gong, Timing; BGI-Shenzhen, Shenzhen 518083, China; Liu, Hongde; State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China; Zhang, Dejin; State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China; Fang, Lin; BGI-Shenzhen, Shenzhen 518083, China; Ye, Chen; BGI-Shenzhen, Shenzhen 518083, China; Zhang, Juanbin; BGI-Shenzhen, Shenzhen 518083, China; Hu, Wenbo; State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, 510275 Guanghou, China; Xu, Anlong; State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, 510275 Guanghou, China; Ren, Yuanyuan; BGI-Shenzhen, Shenzhen 518083, China; Zhang, Guojie; BGI-Shenzhen, Shenzhen 518083, China; The Graduate University of Chinese Academy of Sciences, Beijing 100062, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Bruford, Michael W.; Biodiversity and Ecological Processes Group, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Li, Qibin; BGI-Shenzhen, Shenzhen 518083, China; The Graduate University of Chinese Academy of Sciences, Beijing 100062, China; Ma, Lijia; BGI-Shenzhen, Shenzhen 518083, China; The Graduate University of Chinese Academy of Sciences, Beijing 100062, China; Guo, Yiran; BGI-Shenzhen, Shenzhen 518083, China; The Graduate University of Chinese Academy of Sciences, Beijing 100062, China; An, Na; BGI-Shenzhen, Shenzhen 518083, China; Hu, Yujie; BGI-Shenzhen, Shenzhen 518083, China; The Graduate University of Chinese Academy of Sciences, Beijing 100062, China; Zheng, Yang; BGI-Shenzhen, Shenzhen 518083, China; The Graduate University of Chinese Academy of Sciences, Beijing 100062, China; Shi, Yongyong; Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China; Li, Zhiqiang; Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China; Liu, Qing; BGI-Shenzhen, Shenzhen 518083, China; Chen, Yanling; BGI-Shenzhen, Shenzhen 518083, China; Zhao, Jing; BGI-Shenzhen, Shenzhen 518083, China; Qu, Ning; BGI-Shenzhen, Shenzhen 518083, China; Genome Research Institute, Shenzhen University Medical School, Shenzhen 518000, China; Zhao, Shancen; BGI-Shenzhen, Shenzhen 518083, China; Tian, Feng; BGI-Shenzhen, Shenzhen 518083, China; Wang, Xiaoling; BGI-Shenzhen, Shenzhen 518083, China; Wang, Haiyin; BGI-Shenzhen, Shenzhen 518083, China; Xu, Lizhi; BGI-Shenzhen, Shenzhen 518083, China; Liu, Xiao; BGI-Shenzhen, Shenzhen 518083, China; Vinar, Tomas; Department of Applied Informatics, Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynska Dolina, 84248 Bratislava, Slovakia; Wang, Yajun; School of Life Science, Sichuan University, Chengdu 610064, China; Lam, Tak-Wah; Department of Computer Science, The University of Hong Kong, Hong Kong, China; Yiu, Siu-Ming; Department of Computer Science, The University of Hong Kong, Hong Kong, China; Liu, Shiping; South China University of Technology, Guangzhou 510641, China; Zhang, Hemin; China Conservation and Research Centre for the Giant Panda, Wolong Nature Reserve 623006, China; Li, Desheng; China Conservation and Research Centre for the Giant Panda, Wolong Nature Reserve 623006, China; Huang, Yan; China Conservation and Research Centre for the Giant Panda, Wolong Nature Reserve 623006, China; Wang, Xia; BGI-Shenzhen, Shenzhen 518083, China; Yang, Guohua; BGI-Shenzhen, Shenzhen 518083, China; Jiang, Zhi; BGI-Shenzhen, Shenzhen 518083, China; Wang, Junyi; BGI-Shenzhen, Shenzhen 518083, China; Qin, Nan; BGI-Shenzhen, Shenzhen 518083, China; Li, Li; BGI-Shenzhen, Shenzhen 518083, China; Li, Jingxiang; BGI-Shenzhen, Shenzhen 518083, China; Bolund, Lars; BGI-Shenzhen, Shenzhen 518083, China; Kristiansen, Karsten; BGI-Shenzhen, Shenzhen 518083, China; Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark; Wong, Gane Ka-Shu; BGI-Shenzhen, Shenzhen 518083, China; Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E9, Canada; Olson, Maynard; University of Washington Genome Center, Seattle 352145, USA; Zhang, Xiuqing; BGI-Shenzhen, Shenzhen 518083, China; Li, Songgang; BGI-Shenzhen, Shenzhen 518083, China; Yang, Huanming; BGI-Shenzhen, Shenzhen 518083, China; Wang, Jian; BGI-Shenzhen, Shenzhen 518083, China; Wang, Jun; BGI-Shenzhen, Shenzhen 518083, China; Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark
Журнал:
Nature
Дата:
2009
Аннотация:
Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25â gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05â Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7â million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.
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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. 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