Now showing items 1-20 of 45

    • Activation of the PD-1 Pathway Contributes to Immune Escape in EGFR-Driven Lung Tumors 

      Akbay, E; Koyama, S.; Carretero, J.; Altabef, A.; Tchaicha, J. H.; Christensen, Camilla Laulund; Mikse, O. R.; Cherniack, Andrew David; Beauchamp, Ellen Monica; Pugh, T; Wilkerson, M. D.; Fecci, P; Butaney, M.; Reibel, J. B.; Soucheray, M.; Cohoon, T. J.; Janne, Pasi Antero; Meyerson, Matthew Langer; Hayes, D. N.; Shapiro, Geoffrey Ira; Shimamura, T; Sholl, Lynette Marie; Rodig, Scott J.; Freeman, Gordon James; Hammerman, Peter Seth; Dranoff, G; Wong, Kwok-Kin (American Association for Cancer Research (AACR), 2013)
      The success in lung cancer therapy with Programmed Death (PD)-1 blockade suggests that immune escape mechanisms contribute to lung tumor pathogenesis. We identified a correlation between Epidermal Growth Factor Receptor ...
    • 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 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)
    • BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers 

      Abo, Ryan P.; Ducar, Matthew; Garcia, Elizabeth P.; Thorner, Aaron R.; Rojas-Rudilla, Vanesa; Lin, Ling; Sholl, Lynette M.; Hahn, William C.; Meyerson, Matthew; Lindeman, Neal I.; Van Hummelen, Paul; MacConaill, Laura E. (Oxford University Press, 2015)
      Genomic structural variation (SV), a common hallmark of cancer, has important predictive and therapeutic implications. However, accurately detecting SV using high-throughput sequencing data remains challenging, especially ...
    • Cancer Genome Characterization with SNP Array and Whole-Exome Sequencing Analysis 

      Ramos, Alexis (2013-02-25)
      Cancer, the uncontrolled growth of morphologically and genetically abnormal cells in the body, is a major worldwide public health problem and there is a great need for novel insights into this disease. The majority of ...
    • Characterization of DDR2 Inhibitors for the Treatment of DDR2 Mutated Nonsmall Cell Lung Cancer 

      Terai, Hideki; Tan, Li; Beauchamp, Ellen M.; Hatcher, John M.; Liu, Qingsong; Meyerson, Matthew; Gray, Nathanael S.; Hammerman, Peter S. (American Chemical Society, 2015)
      Despite advances in precision medicine approaches over the past decade, the majority of nonsmall cell lung cancers (NSCLCs) are refractory to treatment with targeted small molecule inhibitors. Previous work has identified ...
    • CHROMOTHRIPSIS FROM DNA DAMAGE IN MICRONUCLEI 

      Zhang, Cheng-Zhong; Spektor, Alexander; Cornils, Hauke; Francis, Joshua M.; Jackson, Emily K.; Liu, Shiwei; Meyerson, Matthew; Pellman, David (2015)
      Genome sequencing has uncovered a new mutational phenomenon in cancer and congenital disorders called chromothripsis. Chromothripsis is characterized by extensive genomic rearrangements and an oscillating pattern of DNA ...
    • Colon cancer-derived oncogenic EGFR G724S mutant identified by whole genome sequence analysis is dependent on asymmetric dimerization and sensitive to cetuximab 

      Cho, Jeonghee; Bass, Adam J; Lawrence, Michael S; Cibulskis, Kristian; Cho, Ahye; Lee, Shi-Nai; Yamauchi, Mai; Wagle, Nikhil; Pochanard, Panisa; Kim, Nayoung; Park, Angela KJ; Won, Jonghwa; Hur, Hyung-Suk; Greulich, Heidi; Ogino, Shuji; Sougnez, Carrie; Voet, Douglas; Tabernero, Josep; Jimenez, Jose; Baselga, Jose; Gabriel, Stacey B; Lander, Eric S; Getz, Gad; Eck, Michael J; Park, Woong-Yang; Meyerson, Matthew (BioMed Central, 2014)
      Background: Inhibition of the activated epidermal growth factor receptor (EGFR) with either enzymatic kinase inhibitors or anti-EGFR antibodies such as cetuximab, is an effective modality of treatment for multiple human ...
    • 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 ...
    • Comparison of Prevalence and Types of Mutations in Lung Cancers Among Black and White Populations 

      Campbell, Joshua David; Lathan, Christopher Scott; Sholl, Lynette Marie; Ducar, Matthew; Vega, Mikenah; Sunkavalli, Ashwini; Lin, Ling; Hanna, Megan; Schubert, Laura; Thorner, Aaron; Faris, Nicholas; Williams, David; Osarogiagbon, Raymond U.; van Hummelen, Paul; Meyerson, Matthew Langer; MacConaill, Laura Eleanor (American Medical Association (AMA), 2017)
      Importance Lung cancer is the leading cause of cancer death in the United States in all ethnic and racial groups. The overall death rate from lung cancer is higher in black patients than in white patients. Objective ...
    • Deep Sequencing and Functional Analyses Identify a Role of Fusobacterium Species in Colorectal Tumorigenesis 

      Kostic, Aleksandar David (2013-09-30)
      The tumor microenvironment is a complex community consisting of neoplastic cells, surrounding stromal cells, a broad array of immune cells, and a microbiota. By sheer numbers, the microbiota has its greatest manifestation ...
    • 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 ...
    • Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas 

      Campbell, Joshua D.; Alexandrov, Anton; Kim, Jaegil; Wala, Jeremiah; Berger, Alice H.; Pedamallu, Chandra Sekhar; Shukla, Sachet A.; Guo, Guangwu; Brooks, Angela N.; Murray, Bradley A.; Imielinski, Marcin; Hu, Xin; Ling, Shiyun; Akbani, Rehan; Rosenberg, Mara; Cibulskis, Carrie; Ramachandran, Aruna; Collisson, Eric A.; Kwiatkowski, David J.; Lawrence, Michael S.; Weinstein, John N.; Verhaak, Roel G. W.; Wu, Catherine J.; Hammerman, Peter S.; Cherniack, Andrew D.; Getz, Gad; Artyomov, Maxim N.; Schreiber, Robert; Govindan, Ramaswamy; Meyerson, Matthew (2016)
      To compare lung adenocarcinoma (ADC) and lung squamous cell carcinoma (SqCC) and to identify new drivers of lung carcinogenesis, we examined exome sequences and copy number profiles of 660 lung ADC and 484 lung SqCC ...
    • DNA copy number analysis of metastatic urothelial carcinoma with comparison to primary tumors 

      Bambury, Richard M; Bhatt, Ami S; Riester, Markus; Pedamallu, Chandra Sekhar; Duke, Fujiko; Bellmunt, Joaquim; Stack, Edward C; Werner, Lillian; Park, Rachel; Iyer, Gopa; Loda, Massimo; Kantoff, Philip W; Michor, Franziska; Meyerson, Matthew; Rosenberg, Jonathan E (BioMed Central, 2015)
      Background: To date, there have been no reports characterizing the genome-wide somatic DNA chromosomal copy-number alteration landscape in metastatic urothelial carcinoma. We sought to characterize the DNA copy-number ...
    • 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 ...
    • 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, ...
    • Functional Copy-Number Alterations in Cancer 

      Taylor, Barry S.; Barretina, Jordi; Socci, Nicholas D.; DeCarolis, Penelope; Ladanyi, Marc; Sander, Chris; Gibson, Greg; Meyerson, Matthew Langer; Singer, Samuel (Public Library of Science, 2008)
      Understanding the molecular basis of cancer requires characterization of its genetic defects. DNA microarray technologies can provide detailed raw data about chromosomal aberrations in tumor samples. Computational analysis ...
    • Functional Studies of Candidate Oncogenes in Non-Small Cell Lung Cancer 

      Liao, Rachel Grace (2013-10-17)
      Cancer is a set of complex genetic diseases driven by diverse genomic alterations. The genomic study of cancer has enabled the discovery of novel, targetable events in almost all cancer types and in turn, has led to the ...
    • 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 ...
    • Genetic and Chemical Modifiers of EGFR Dependence in Non-Small Cell Lung Cancer 

      Sharifnia, Tanaz (2014-02-25)
      The term `oncogene addiction' has been used to describe the phenomenon whereby tumor cells exhibit singular reliance on an oncogene or oncogenic pathway for their survival, despite the accumulation of multiple genetic ...