Browsing by Author "Beroukhim, Rameen"

Now showing items 1-20 of 31

    • Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis 

      LaFramboise, Thomas; Weir, Barbara Ann; Zhao, Xiaojun; Beroukhim, Rameen; Li, Cheng; Harrington, David Paul; Sellers, William R; Meyerson, Matthew Langer (Public Library of Science, 2005)
      Amplification, deletion, and loss of heterozygosity of genomic DNA are hallmarks of cancer. In recent years a variety of studies have emerged measuring total chromosomal copy number at increasingly high resolution. Similarly, ...

    • Amplification of Chromosomal Segment 4q12 in Non-Small Cell Lung Cancer 

      Ramos, Alex H.; Dutt, Amit; Mermel, Craig; Perner, Sven; Cho, Jeonghee; LaFargue, Christopher J.; Johnson, Laura A.; Stiedl, Ann-Cathrin; Tanaka, Kumiko E.; Bass, Adam; Barretina, Jordi; Weir, Barbara A.; Beroukhim, Rameen; Thomas, Roman K.; Minna, John D.; Chirieac, Lucian; Lindeman, Neal; Giordano, Thomas J.; Beer, David G.; Wagner, Patrick; Wistuba, Ignacio I.; Rubin, Mark A.; Meyerson, Matthew (Informa UK Limited, 2009-11-01)
      In cancer, proto-oncogenes are often altered by genomic amplification. Here we report recurrent focal amplifications of chromosomal segment 4q12 overlapping the proto-oncogenes PDGFRA and KIT in non-small cell lung cancer ...

    • Amplification of phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis 

      Locasale, J.; Grassian, Alexandra; Beroukhim, Rameen; Meyerson, Matthew Langer; Wagner, Gerhard; Asara, John M.; Brugge, Joan S.; Vander Heiden, Matthew George; Cantley, Lewis C. (BioMed Central, 2012)

    • Characterizing the Cancer Genome in Lung Adenocarcinoma 

      Weir, Barbara A.; Woo, Michele S.; Getz, Gad; Perner, Sven; Ding, Li; Beroukhim, Rameen; Lin, William; Province, Michael A.; Kraja, Aldi T.; Johnson, Laura A.; Shah, Kinjal; Sato, Mitsuo; Thomas, Roman K.; Barletta, Justine; Borecki, Ingrid B.; Broderick, Stephen; Chang, Andrew C.; Chiang, Derek Y.; Chirieac, Lucian; Cho, Jeonghee; Fujii, Yoshitaka; Gazdar, Adi F.; Giordano, Thomas J.; Greulich, Heidi; Hanna, Megan; Johnson, Bruce; Kris, Mark G.; Lash, Alex; Lin, Ling; Lindeman, Neal; Mardis, Elaine R.; McPherson, John D.; Minna, John D.; Morgan, Margaret B.; Nadel, Mark; Orringer, Mark B.; Osborne, John R.; Ozenberger, Brad; Ramos, Alex H.; Robinson, James; Roth, Jack A.; Rusch, Valerie; Sasaki, Hidefumi; Shepherd, Frances A.; Sougnez, Carrie; Spitz, Margaret R.; Tsao, Ming-Sound; Twomey, David; Verhaak, Roel G. W.; Weinstock, George; Wheeler, David A.; Winckler, Wendy; Yoshizawa, Akihiko; Yu, Soyoung; Zakowski, Maureen F.; Zhang, Qunyuan; Beer, David G.; Wistuba, Ignacio I.; Watson, Mark A.; Garraway, Levi A.; Ladanyi, Marc; Travis, William D.; Pao, William; Rubin, Mark A; Gabriel, Stacey; Gibbs, Richard A.; Varmus, Harold E.; Wilson, Richard K.; Lander, Eric; Meyerson, Matthew (Springer Science and Business Media LLC, 2007-12-06)
      Somatic alterations in cellular DNA underlie almost all human cancers1. The prospect of targeted therapies2 and the development of high-resolution, genome-wide approaches3–8 are now spurring systematic efforts to characterize ...

    • Epidermal Growth Factor Receptor Activation in Glioblastoma through Novel Missense Mutations in the Extracellular Domain 

      Vivanco, Igor; Feng, Whei L; Yoshimoto, Koji; King, Jennifer C; Nghiemphu, Phioanh; Yuza, Yuki; Xu, Qing; Thomas, Roman K; Peck, Timothy C; Linhart, David J; Glatt, Karen A; Getz, Gad; Onofrio, Robert; Ziaugra, Liuda; Levine, Ross L; Gabriel, Stacey; Kawaguchi, Tomohiro; O'Neill, Keith; Khan, Haumith; Liau, Linda M; Nelson, Stanley F; Rao, P. Nagesh; Mischel, Paul; Pieper, Russell O; Cloughesy, Tim; Leahy, Daniel J; Sellers, William R; Sawyers, Charles L; Mellinghoff, Ingo K; Lee, Jeffrey C.; Beroukhim, Rameen; Huang, Julie; DeBiasi, Ralph Michael; Greulich, Heidi E.; Paez, J. Guillermo; Meyerson, Matthew Langer (Public Library of Science, 2006)
      Background: Protein tyrosine kinases are important regulators of cellular homeostasis with tightly controlled catalytic activity. Mutations in kinase-encoding genes can relieve the autoinhibitory constraints on kinase ...

    • Exome and whole genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity 

      Dulak, Austin M.; Stojanov, Petar; Peng, Shouyong; Lawrence, Michael S.; Fox, Cameron; Stewart, Chip; Bandla, Santhoshi; Imamura, Yu; Schumacher, Steven E.; Shefler, Erica; McKenna, Aaron; Cibulskis, Kristian; Sivachenko, Andrey; Carter, Scott L.; Saksena, Gordon; Voet, Douglas; Ramos, Alex H.; Auclair, Daniel; Thompson, Kristin; Sougnez, Carrie; Onofrio, Robert C.; Guiducci, Candace; Beroukhim, Rameen; Zhou, David; Lin, Lin; Lin, Jules; Reddy, Rishindra; Chang, Andrew; Luketich, James D.; Pennathur, Arjun; Ogino, Shuji; Golub, Todd R.; Gabriel, Stacey B.; Lander, Eric S.; Beer, David G.; Godfrey, Tony E.; Getz, Gad; Bass, Adam J. (2013)
      The incidence of esophageal adenocarcinoma (EAC) has risen 600% over the last 30 years. With a five-year survival rate of 15%, identification of new therapeutic targets for EAC is greatly important. We analyze the mutation ...

    • Exploring Cancer's Fractured Genomic Landscape: Searching for Cancer Drivers and Vulnerabilities in Somatic Copy Number Alterations 

      Zack, Travis Ian (2014-10-21)
      Somatic copy number alterations (SCNAs) are a class of alterations that lead to deviations from diploidy in developing and established tumors. A feature that distinguishes SCNAs from other alterations is their genomic ...

    • Functional characterization of genetic alterations in cancer 

      Kim, Eejung (2016-05-18)
      The comprehensive identification of genetic alterations is critical to understanding the pathophysiology of cancer. Recent advances in sequencing technology have enabled the detailed description of cancer genomes. However, ...

    • Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis 

      Dulak, A. M.; Schumacher, S. E.; van Lieshout, J.; Imamura, Y.; Fox, Cameron; Shim, B.; Ramos, A. H.; Saksena, G.; Baca, Sylvan Charles; Baselga, J.; Tabernero, J.; Barretina, J.; Enzinger, Peter C.; Corso, G.; Roviello, F.; Lin, Lin; Bandla, S.; Luketich, J. D.; Pennathur, A.; Meyerson, Matthew Langer; Ogino, Shuji; Shivdasani, Ramesh Arjun; Beer, Dennis J; Godfrey, T. E.; Beroukhim, Rameen; Bass, Adam Joel (American Association for Cancer Research (AACR), 2012)
      A more detailed understanding of the somatic genetic events that drive gastrointestinal adenocarcinomas is necessary to improve diagnosis and therapy. Using data from high-density genomic profiling arrays, we conducted an ...

    • The genomic landscape and evolution of endometrial carcinoma progression and abdominopelvic metastasis 

      Gibson, William J.; Hoivik, Erling A.; Halle, Mari K.; Taylor-Weiner, Amaro; Cherniack, Andrew D.; Berg, Anna; Holst, Frederik; Zack, Travis I.; Werner, Henrica M. J.; Staby, Kjersti M.; Rosenberg, Mara; Stefansson, Ingunn M.; Kusonmano, Kanthida; Chevalier, Aaron; Mauland, Karen K.; Trovik, Jone; Krakstad, Camilla; Giannakis, Marios; Hodis, Eran; Woie, Kathrine; Bjorge, Line; Vintermyr, Olav K.; Wala, Jeremiah A.; Lawrence, Michael S.; Getz, Gad; Carter, Scott L.; Beroukhim, Rameen; Salvesen, Helga B. (2016)
      Recent studies have detailed the genomic landscape of primary endometrial cancers, but their evolution into metastases has not been characterized. We performed whole-exome sequencing of 98 tumor biopsies including complex ...

    • Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations 

      Brastianos, Priscilla K.; Horowitz, Peleg M.; Santagata, Sandro; Jones, Robert T.; McKenna, Aaron; Getz, Gad; Ligon, Keith L.; Palescandolo, Emanuele; Van Hummelen, Paul; Ducar, Matthew D.; Raza, Alina; Sunkavalli, Ashwini; MacConaill, Laura E.; Stemmer-Rachamimov, Anat O.; Louis, David N.; Hahn, William C.; Dunn, Ian F.; Beroukhim, Rameen (2013)
      Meningiomas are the most common primary nervous system tumor. The tumor suppressor NF2 is disrupted in approximately half of meningiomas1 but the complete spectrum of genetic changes remains undefined. We performed ...

    • The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset 

      Ceol, Craig J.; Houvras, Yariv; Jane-Valbuena, Judit; Bilodeau, Steve; Orlando, David A.; Battisti, Valentine; Fritsch, Lauriane; Lin, William Michael; Hollmann, Travis J.; Ferré, Fabrizio; Bourque, Caitlin; Burke, Christopher J.; Turner, Laura; Uong, Audrey; Johnson, Laura A.; Beroukhim, Rameen; Mermel, Craig Harold; Loda, Massimo; Ait-Si-Ali, Slimane; Garraway, Levi Alexander; Young, Richard A.; Zon, Leonard Ira (Nature Publishing Group, 2011)

    • Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays 

      Park, Yuhyun; Hao, Ke; Zhao, Xiaojun; Mellinghoff, Ingo K; Hofer, Matthias D; Descazeaud, Aurelien; Rubin, Mark A; Sellers, William R; Bourne, Philip; Beroukhim, Rameen; Lin, Ming; Garraway, Levi Alexander; Fox, Edward Alvin; Hochberg, Ephraim Paul; Meyerson, Matthew Langer; Wong, Wing H; Li, Cheng (Public Library of Science, 2006)
      Loss of heterozygosity (LOH) of chromosomal regions bearing tumor suppressors is a key event in the evolution of epithelial and mesenchymal tumors. Identification of these regions usually relies on genotyping tumor and ...

    • Integrated Genomic Analysis of the 8q24 Amplification in Endometrial Cancers Identifies ATAD2 as Essential to MYC-Dependent Cancers 

      Raeder, Maria B.; Birkeland, Even; Trovik, Jone; Krakstad, Camilla; Shehata, Shyemaa; Schumacher, Steven; Zack, Travis Ian; Krohn, Antje; Werner, Henrica MJ.; Moody, Susan E; Wik, Elisabeth; Stefansson, Ingunn M.; Holst, Frederik; Oyan, Anne M.; Tamayo, Pablo; Mesirov, Jill; Kalland, Karl H.; Akslen, Lars A.; Simon, Ronald; Beroukhim, Rameen; Salvesen, Helga B. (Public Library of Science, 2013)
      Chromosome 8q24 is the most commonly amplified region across multiple cancer types, and the typical length of the amplification suggests that it may target additional genes to MYC. To explore the roles of the genes most ...

    • Interpreting Cancer Genomes Using Systematic Host Perturbations by Tumour Virus Proteins 

      Rozenblatt-Rosen, Orit; Deo, Rahul C.; Dricot, Amélie; Askenazi, Manor; Tavares, Maria; Abderazzaq, Fieda; Byrdsong, Danielle; Correll, Mick; Fan, Changyu; Feltkamp, Mariet C.; Franchi, Rachel; Garg, Brijesh K.; Gulbahce, Natali; Hao, Tong; Korkhin, Anna; Litovchick, Larisa; Mar, Jessica C.; Pak, Theodore R.; Rabello, Sabrina; Rubio, Renee; Shen, Yun; Tasan, Murat; Wanamaker, Shelly; Roecklein-Canfield, Jennifer; Johannsen, Eric; Barabási, Albert-László; Padi, Megha; Adelmant, Guillaume; Calderwood, Michael A; Rolland, Thomas; Grace, Miranda; Pevzner, Samuel; Carvunis, Anne-Ruxandra; Chen, Alyce Aura; Cheng, Jingwei; Duarte, Melissa; Ficarro, Scott; Holthaus, Amy Marie; James, Robert; Singh, Saurav; Spangle, Jennifer Marie; Webber, James T.; Beroukhim, Rameen; Kieff, Elliott D.; Cusick, Michael; Hill, David E.; Munger, Karl; Marto, Jarrod; Quackenbush, John; Roth, Frederick Phillip; DeCaprio, James A.; Vidal, Marc (Nature Publishing Group, 2012)
      Genotypic differences greatly influence susceptibility and resistance to disease. Understanding genotype-phenotype relationships requires that phenotypes be viewed as manifestations of network properties, rather than simply ...

    • Major Copy Proportion Analysis of Tumor Samples Using SNP Arrays 

      Li, Cheng; Beroukhim, Rameen; Weir, Barbara Ann; Winckler, Wendy; Garraway, Levi Alexander; Sellers, William R; Meyerson, Matthew Langer (BioMed Central, 2008)
      Background: Single nucleotide polymorphisms (SNPs) are the most common genetic variations in the human genome and are useful as genomic markers. Oligonucleotide SNP microarrays have been developed for high-throughput ...

    • MAPK activation and HRAS mutation identified in pituitary spindle cell oncocytoma 

      Miller, Michael B.; Bi, Wenya Linda; Ramkissoon, Lori A.; Kang, Yun Jee; Abedalthagafi, Malak; Knoff, David S.; Agarwalla, Pankaj K.; Wen, Patrick Y.; Reardon, David A.; Alexander, Brian M.; Laws, Edward R.; Dunn, Ian F.; Beroukhim, Rameen; Ligon, Keith L.; Ramkissoon, Shakti H. (Impact Journals LLC, 2016)
      Pituitary spindle cell oncocytoma (SCO) is an uncommon primary pituitary neoplasm that presents with mass effect on adjacent neurovascular structures, similar to non-hormone-producing pituitary adenomas. To determine the ...

    • A Mathematical Methodology for Determining the Temporal Order of Pathway Alterations Arising during Gliomagenesis 

      Cheng, Yu-Kang; Beroukhim, Rameen; Levine, Ross L.; Mellinghoff, Ingo K.; Holland, Eric C.; Michor, Franziska L. (Public Library of Science, 2012)
      Human cancer is caused by the accumulation of genetic alterations in cells. Of special importance are changes that occur early during malignant transformation because they may result in oncogene addiction and thus represent ...

    • MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy 

      Neupane, Manish; Clark, Allison Paige; Landini, S.; Birkbak, N; Eklund, A. C.; Lim, E.; Culhane, Aedin; Barry, William T.; Schumacher, Sandra Kay; Beroukhim, Rameen; Szallasi, Zoltan; Vidal, Marc; Hill, David E.; Silver, Daniel P. (American Association for Cancer Research (AACR), 2015)
      An unbiased genome-scale screen for unmutated genes that drive cancer growth when overexpressed identified MECP2 as a novel oncogene. MECP2 resides in a region of the Xchromosome that is significantly amplified across 18% ...

    • Molecular profiling of endometrial carcinoma precursor, primary and metastatic lesions suggests different targets for treatment in obese compared to non-obese patients 

      Berg, Anna; Hoivik, Erling A.; Mjøs, Siv; Holst, Frederik; Werner, Henrica M. J.; Tangen, Ingvild L.; Taylor-Weiner, Amaro; Gibson, William J.; Kusonmano, Kanthida; Wik, Elisabeth; Trovik, Jone; Halle, Mari K.; Øyan, Anne M.; Kalland, Karl-Henning; Cherniack, Andrew D.; Beroukhim, Rameen; Stefansson, Ingunn; Mills, Gordon B.; Krakstad, Camilla; Salvesen, Helga B. (Impact Journals LLC, 2015)
      Obesity is linked to increased incidence of endometrioid endometrial cancer (EEC) and complex atypical hyperplasia (CAH). We here explore pattern and sequence of molecular alterations characterizing endometrial carcinogenesis ...