Now showing items 1-20 of 31

    • Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly dividing de‐differentiated state 

      Fallahi‐Sichani, Mohammad; Becker, Verena; Izar, Benjamin; Baker, Gregory J; Lin, Jia‐Ren; Boswell, Sarah A; Shah, Parin; Rotem, Asaf; Garraway, Levi A; Sorger, Peter K (John Wiley and Sons Inc., 2017)
      Abstract Treatment of BRAF‐mutant melanomas with MAP kinase pathway inhibitors is paradigmatic of the promise of precision cancer therapy but also highlights problems with drug resistance that limit patient benefit. We use ...
    • Assessing the clinical utility of cancer genomic and proteomic data across tumor types 

      Yuan, Yuan; Van Allen, Eliezer M.; Omberg, Larsson; Wagle, Nikhil; Amin-Mansour, Ali; Sokolov, Artem; Byers, Lauren A.; Xu, Yanxun; Hess, Kenneth R.; Diao, Lixia; Han, Leng; Huang, Xuelin; Lawrence, Michael S.; Weinstein, John N.; Stuart, Josh M.; Mills, Gordon B.; Garraway, Levi A.; Margolin, Adam A.; Getz, Gad; Liang, Han (2014)
      Molecular profiling of tumors promises to advance the clinical management of cancer, but the benefits of integrating molecular data with traditional clinical variables have not been systematically studied. Here we ...
    • Colorectal Cancers from Distinct Ancestral Populations Show Variations in BRAF Mutation Frequency 

      Hanna, Megan C.; Go, Christina; Roden, Christine; Jones, Robert T.; Pochanard, Panisa; Javed, Ahmed Yasir; Javed, Awais; Mondal, Chandrani; Palescandolo, Emanuele; Van Hummelen, Paul; Hatton, Charles; Bass, Adam J.; Chun, Sung Min; Na, Deuk Chae; Kim, Tae-Im; Jang, Se Jin; Osarogiagbon, Raymond U.; Hahn, William C.; Meyerson, Matthew; Garraway, Levi A.; MacConaill, Laura E. (Public Library of Science, 2013)
      It has been demonstrated for some cancers that the frequency of somatic oncogenic mutations may vary in ancestral populations. To determine whether key driver alterations might occur at different frequencies in colorectal ...
    • Discovery and saturation analysis of cancer genes across 21 tumor types 

      Lawrence, Michael S.; Stojanov, Petar; Mermel, Craig H.; Garraway, Levi A.; Golub, Todd R.; Meyerson, Matthew; Gabriel, Stacey B.; Lander, Eric S.; Getz, Gad (2014)
      Summary While a few cancer genes are mutated in a high proportion of tumors of a given type (>20%), most are mutated at intermediate frequencies (2–20%). To explore the feasibility of creating a comprehensive catalog of ...
    • Divergent clonal evolution of castration resistant neuroendocrine prostate cancer 

      Beltran, Himisha; Prandi, Davide; Mosquera, Juan Miguel; Benelli, Matteo; Puca, Loredana; Cyrta, Joanna; Marotz, Clarisse; Giannopoulou, Eugenia; Chakravarthi, Balabhadrapatruni V.S.K.; Varambally, Sooryanarayana; Tomlins, Scott A.; Nanus, David M.; Tagawa, Scott T.; Van Allen, Eliezer M.; Elemento, Olivier; Sboner, Andrea; Garraway, Levi A.; Rubin, Mark A.; Demichelis, Francesca (2016)
      An increasingly recognized resistance mechanism to androgen receptor (AR)-directed therapy in prostate cancer involves epithelial plasticity, wherein tumor cells demonstrate low to absent AR expression and often neuroendocrine ...
    • The Genomic Landscape of Prostate Cancer 

      Baca, Sylvan Charles; Garraway, Levi Alexander (Frontiers Research Foundation, 2012)
      Prostate cancer is a common malignancy in men, with a markedly variable clinical course. Somatic alterations in DNA drive the growth of prostate cancers and may underlie the behavior of aggressive versus indolent tumors. ...
    • Genotyping Cancer-Associated Genes in Chordoma Identifies Mutations in Oncogenes and Areas of Chromosomal Loss Involving CDKN2A, PTEN, and SMARCB1 

      Choy, Edwin; MacConaill, Laura E.; Cote, Gregory M.; Le, Long P.; Shen, Jacson K.; Nielsen, Gunnlaugur P.; Iafrate, Anthony J.; Garraway, Levi A.; Hornicek, Francis J.; Duan, Zhenfeng (Public Library of Science, 2014)
      The molecular mechanisms underlying chordoma pathogenesis are unknown. We therefore sought to identify novel mutations to better understand chordoma biology and to potentially identify therapeutic targets. Given the ...
    • 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)
    • The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine 

      Garofalo, Andrea; Sholl, Lynette; Reardon, Brendan; Taylor-Weiner, Amaro; Amin-Mansour, Ali; Miao, Diana; Liu, David; Oliver, Nelly; MacConaill, Laura; Ducar, Matthew; Rojas-Rudilla, Vanesa; Giannakis, Marios; Ghazani, Arezou; Gray, Stacy; Janne, Pasi; Garber, Judy; Joffe, Steve; Lindeman, Neal; Wagle, Nikhil; Garraway, Levi A.; Van Allen, Eliezer M. (BioMed Central, 2016)
      Background: The diversity of clinical tumor profiling approaches (small panels to whole exomes with matched or unmatched germline analysis) may engender uncertainty about their benefits and liabilities, particularly in ...
    • 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 genetic and pharmacologic interrogation of rare cancers 

      Hong, Andrew L.; Tseng, Yuen-Yi; Cowley, Glenn S.; Jonas, Oliver; Cheah, Jaime H.; Kynnap, Bryan D.; Doshi, Mihir B.; Oh, Coyin; Meyer, Stephanie C.; Church, Alanna J.; Gill, Shubhroz; Bielski, Craig M.; Keskula, Paula; Imamovic, Alma; Howell, Sara; Kryukov, Gregory V.; Clemons, Paul A.; Tsherniak, Aviad; Vazquez, Francisca; Crompton, Brian D.; Shamji, Alykhan F.; Rodriguez-Galindo, Carlos; Janeway, Katherine A.; Roberts, Charles W. M.; Stegmaier, Kimberly; van Hummelen, Paul; Cima, Michael J.; Langer, Robert S.; Garraway, Levi A.; Schreiber, Stuart L.; Root, David E.; Hahn, William C.; Boehm, Jesse S. (Nature Publishing Group, 2016)
      Identifying therapeutic targets in rare cancers remains challenging due to the paucity of established models to perform preclinical studies. As a proof-of-concept, we developed a patient-derived cancer cell line, CLF-PED-015-T, ...
    • An Interactive Resource to Identify Cancer Genetic and Lineage Dependencies Targeted by Small Molecules 

      Basu, Amrita; Bodycombe, Nicole E.; Cheah, Jaime H.; Price, Edmund V.; Liu, Ke; Schaefer, Giannina Ines; Ebright, Richard Yon; Stewart, Michelle L.; Ito, Daisuke; Wang, Stephanie; Bracha, Abigail L.; Liefeld, Ted; Wawer, Mathias; Gilbert, Joshua C.; Wilson, Andrew J.; Stransky, Nicolas; Kryukov, Gregory V.; Dancik, Vlado; Barretina, Jordi; Garraway, Levi Alexander; Hon, C. Suk-Yee; Munoz, Benito; Bittker, Joshua A.; Stockwell, Brent R.; Khabele, Dineo; Stern, Andrew M.; Clemons, Paul A.; Shamji, Alykhan F.; Schreiber, Stuart L. (Elsevier BV, 2013)
      The high rate of clinical response to protein-kinase-targeting drugs matched to cancer patients with specific genomic alterations has prompted efforts to use cancer cell line (CCL) profiling to identify additional biomarkers ...
    • The landscape of somatic mutations in primary prostate adenocarcinoma 

      Baca, Sylvan Charles (2013-10-08)
      Prostate cancer is the second leading cause of cancer deaths among men. Targeted analyses of DNA from prostate cancers have identified recurrent somatic alterations that promote tumor growth and survival. Only recently, ...
    • Locally Disordered Methylation Forms the Basis of Intratumor Methylome Variation in Chronic Lymphocytic Leukemia 

      Landau, Dan Avi; Clement, Kendell; Ziller, Michael Johannes; Boyle, Patrick; Fan, Jean; Gu, Hongcang; Stevenson, Kristen; Sougnez, Carrie; Wang, Lili; Li, Shuqiang; Kotliar, Dylan; Zhang, Wandi; Ghandi, Mahmoud; Garraway, Levi Alexander; Fernandes, Stacey M.; Livak, Kenneth J.; Gabriel, Stacey; Gnirke, Andreas; Lander, Eric Steven; Brown, Jennifer Ruth; Neuberg, Donna S.; Kharchenko, Peter Vasili; Hacohen, Nir; Getz, Gad A; Meissner, Alexander; Wu, Catherine J. (Elsevier BV, 2014)
      Intratumoral heterogeneity plays a critical role in tumor evolution. To define the contribution of DNA methylation to heterogeneity within tumors, we performed genome-scale bisulfite sequencing of 104 primary chronic ...
    • Long-term Benefit of PD-L1 Blockade in Lung Cancer Associated with JAK3 Activation 

      Van Allen, Eliezer Mendel; Golay, H. G.; Liu, Yan; Koyama, S.; Wong, Kwok-Kin; Taylor-Weiner, Amaro; Giannakis, Marios; Harden, M.; Rojas-Rudilla, V.; Chevalier, A.; Thai, T.; Lydon, C.; Mach, S.; Wong, J. A.; Rabin, A. R.; Helmkamp, J.; Sholl, Lynette Marie; Carter, Scott Lambert; Oxnard, Geoffrey Raymond; Janne, Pasi Antero; Getz, Gad A; Lindeman, Neal I.; Hammerman, Peter Seth; Garraway, Levi Alexander; Hodi, Frank Stephen; Rodig, Scott J.; Dranoff, G; Wong, Kwok-Kin; Barbie, David Allen (American Association for Cancer Research (AACR), 2015)
      PD-1 immune checkpoint blockade occasionally results in durable clinical responses in advanced metastatic cancers. However, mechanism-based predictors of response to this immunotherapy remain incompletely characterized. ...
    • 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 ...
    • Mechanisms and Vulnerabilities of Mutant SWI/SNF Complexes in Cancer 

      Walsh, Katherine Helming (2015-05-06)
      Genes encoding subunits of the SWI/SNF chromatin remodeling complex are frequently mutated in a wide variety of cancers, but the mechanism of cancer formation following SWI/SNF subunit mutation is not known. As a result, ...
    • Mechanisms of Resistance to MAPK Pathway Inhibition in RAS-Mutant Cancers 

      Wang, Belinda (2016-05-03)
      The RAS family of genes are among the most frequently mutated genes in human cancers, including nearly all pancreatic cancers, ~40% of colorectal cancers, and ~30% of lung cancers. Although most RAS-mutant cancers depend ...
    • A melanocyte lineage program confers resistance to MAP kinase pathway inhibition 

      Johannessen, Cory M.; Johnson, Laura A.; Piccioni, Federica; Townes, Aisha; Frederick, Dennie T.; Donahue, Melanie K.; Narayan, Rajiv; Flaherty, Keith T.; Wargo, Jennifer A.; Root, David E.; Garraway, Levi A. (2014)
      BRAFV600E-mutant malignant melanomas depend on RAF/MEK/ERK (MAPK) signaling for tumor cell growth1. RAF and MEK inhibitors show remarkable clinical efficacy in BRAFV600E melanoma2, 3; however, resistance to these agents ...
    • Melanoma genome sequencing reveals frequent PREX2 mutations 

      Berger, Michael F.; Hodis, Eran; Heffernan, Timothy P.; Deribe, Yonathan Lissanu; Lawrence, Michael S.; Protopopov, Alexei; Ivanova, Elena; Watson, Ian R.; Nickerson, Elizabeth; Ghosh, Papia; Zhang, Hailei; Zeid, Rhamy; Ren, Xiaojia; Cibulskis, Kristian; Sivachenko, Andrey Y.; Wagle, Nikhil; Sucker, Antje; Sougnez, Carrie; Onofrio, Robert; Ambrogio, Lauren; Auclair, Daniel; Fennell, Timothy; Carter, Scott L.; Drier, Yotam; Stojanov, Petar; Singer, Meredith A.; Voet, Douglas; Jing, Rui; Saksena, Gordon; Barretina, Jordi; Ramos, Alex H.; Pugh, Trevor J.; Stransky, Nicolas; Parkin, Melissa; Winckler, Wendy; Mahan, Scott; Ardlie, Kristin; Baldwin, Jennifer; Wargo, Jennifer; Schadendorf, Dirk; Meyerson, Matthew; Gabriel, Stacey B.; Golub, Todd R.; Wagner, Stephan N.; Lander, Eric S.; Getz, Gad; Chin, Lynda; Garraway, Levi A. (2012)
      Melanoma is notable for its metastatic propensity, lethality in the advanced setting, and association with ultraviolet (UV) exposure early in life1. To obtain a comprehensive genomic view of melanoma, we sequenced the ...