Now showing items 21-30 of 30

    • Oncologists' and Cancer Patients' Views on Whole-Exome Sequencing and Incidental Findings: Results from The CanSeq Study 

      Gray, Stacy W.; Park, Elyse R.; Najita, Julie; Martins, Yolanda; Traeger, Lara; Bair, Elizabeth; Gagne, Joshua; Garber, Judy; Jänne, Pasi A.; Lindeman, Neal; Lowenstein, Carol; Oliver, Nelly; Sholl, Lynette; Van Allen, Eliezer M.; Wagle, Nikhil; Wood, Sam; Garraway, Levi; Joffe, Steven (2016)
      Purpose While targeted sequencing improves outcomes for many cancer patients, how somatic and germline whole-exome sequencing (WES) will integrate into care remains uncertain. Methods: We conducted surveys and interviews, ...
    • Profiling Critical Cancer Gene Mutations in Clinical Tumor Samples 

      Campbell, Catarina D.; Kehoe, Sarah M.; Hatton, Charles; Niu, Lili; Yao, Keluo; Hanna, Megan; Mondal, Chandrani; Luongo, Lauren; Baker, Alissa C.; Philips, Juliet; Goff, Deborah J.; Rubin, Mark A.; Corso, Gianni; Roviello, Franco; MacConaill, Laura Eleanor; Bass, Adam Joel; Davis, Matthew J; Emery, Caroline Margaret; Fiorentino, Michelangelo; Polyak, Kornelia; Chan, Jennifer Ang; Wang, Yufang; Fletcher, Jonathan A.; Santagata, Sandro; Shivdasani, Ramesh Arjun; Kieran, Mark W.; Ligon, Keith Lloyd; Stiles, Charles Dean; Hahn, William C.; Meyerson, Matthew Langer; Garraway, Levi Alexander; Jones, Chris (Public Library of Science, 2009)
      Background: Detection of critical cancer gene mutations in clinical tumor specimens may predict patient outcomes and inform treatment options; however, high-throughput mutation profiling remains underdeveloped as a diagnostic ...
    • Rapid Intraoperative Molecular Characterization of Glioma 

      Shankar, Ganesh Mani; Francis, Joshua M.; Rinne, Mikael Lee; Ramkissoon, Shakti; Huang, Franklin W; Venteicher, Andrew S; Akama-Garren, Elliot H.; Kang, Yun Jee; Lelic, Nina; Kim, James C.; Brown, Loreal E.; Charbonneau, Sarah K; Golby, Alexandra Jacqueline; Sekhar Pedamallu, Chandra; Hoang, Mai P; Sullivan, Ryan Joseph; Cherniack, Andrew D.; Garraway, Levi Alexander; Stemmer-Rachamimov, Anat; Reardon, David Allen; Wen, Patrick Yung Chih; Brastianos, Priscilla Kalliope; Curry, William Thomas; Barker, Frederick George; Hahn, William Chun; Nahed, Brian Vala; Ligon, Keith Lloyd; Louis, David N.; Cahill, Daniel P.; Meyerson, Matthew Langer (American Medical Association (AMA), 2015)
      IMPORTANCE: Conclusive intraoperative pathologic confirmation of diffuse infiltrative glioma guides the decision to pursue definitive neurosurgical resection. Establishing the intraoperative diagnosis by histologic analysis ...
    • Reactivation of ERK Signaling Causes Resistance to EGFR Kinase Inhibitors 

      Ercan, Dalia; Xu, Chunxiao; Yanagita, Masahiko; Monast, Calixte S.; Pratilas, Christine A.; Montero, Joan; Butaney, Mohit; Shimamura, Takeshi; Sholl, Lynette Marie; Ivanova, Elena; Tadi, Madhavi; Rogers, Andrew; Repellin, Claire; Capelletti, Marzia; Maertens, Ophelia; Goetz, Eva Marie; Letai, Anthony George; Garraway, Levi Alexander; Lazzara, Matthew J.; Rosen, Neal; Gray, Nathanael Schiander; Wong, Kwok-Kin; Janne, Pasi Antero (American Association for Cancer Research (AACR), 2012)
      The clinical efficacy of EGFR kinase inhibitors is limited by the development of drug resistance. The irreversible EGFR kinase inhibitor WZ4002 is effective against the most common mechanism of drug resistance mediated by ...
    • Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair 

      Polak, Paz; Lawrence, Michael S.; Haugen, Eric; Stoletzki, Nina; Stojanov, Petar; Thurman, Robert E; Garraway, Levi A.; Mirkin, Sergei; Getz, Gad; Stamatoyannopoulos, John A.; Sunyaev, Shamil R. (2014)
      Carcinogenesis and neoplastic progression are mediated by the accumulation of somatic mutations. Here we report that the local density of somatic mutations in cancer genomes is highly reduced specifically in accessible ...
    • SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines 

      Demichelis, Francesca; Greulich, Heidi E.; Macoska, Jill A.; Beroukhim, Rameen; Sellers, William R.; Garraway, Levi Alexander; Rubin, Mark A. (Oxford University Press, 2008)
      Translational research hinges on the ability to make observations in model systems and to implement those findings into clinical applications, such as the development of diagnostic tools or targeted therapeutics. Tumor ...
    • Systematic approaches to overcoming limitations of MAPK pathway inhibition in melanoma 

      Konieczkowski, David Joseph (2013-10-15)
      Metastatic melanoma is an aggressive, incurable cancer with historically few therapeutic options. The discovery that 60% of melanomas harbor the oncogenic BRAF_V600E mutation, which constitutively activates the MAPK ...
    • Targeted Next-Generation Sequencing of a Cancer Transcriptome Enhances Detection of Sequence Variants and Novel Fusion Transcripts 

      Levin, Joshua Z; Berger, Michael F; Adiconis, Xian; Rogov, Peter; Melnikov, Alexandre; Fennell, Timothy; Nusbaum, Chad; Garraway, Levi Alexander; Gnirke, Andreas (BioMed Central, 2009)
      Targeted RNA-Seq combines next-generation sequencing with capture of sequences from a relevant subset of a transcriptome. When testing by capturing sequences from a tumor cDNA library by hybridization to oligonucleotide ...
    • Unraveling the clonal hierarchy of somatic genomic aberrations 

      Prandi, Davide; Baca, Sylvan C; Romanel, Alessandro; Barbieri, Christopher E; Mosquera, Juan-Miguel; Fontugne, Jacqueline; Beltran, Himisha; Sboner, Andrea; Garraway, Levi A; Rubin, Mark A; Demichelis, Francesca (BioMed Central, 2014)
      Defining the chronology of molecular alterations may identify milestones in carcinogenesis. To unravel the temporal evolution of aberrations from clinical tumors, we developed CLONET, which upon estimation of tumor admixture ...
    • Whole-exome sequencing and clinical interpretation of FFPE tumor samples to guide precision cancer medicine 

      Allen, Eliezer M. Van; Wagle, Nikhil; Stojanov, Petar; Perrin, Danielle L.; Cibulskis, Kristian; Marlow, Sara; Jane-Valbuena, Judit; Friedrich, Dennis C.; Kryukov, Gregory; Carter, Scott L.; McKenna, Aaron; Sivachenko, Andrey; Rosenberg, Mara; Kiezun, Adam; Voet, Douglas; Lawrence, Michael; Lichtenstein, Lee T.; Gentry, Jeff G.; Huang, Franklin W.; Fostel, Jennifer; Farlow, Deborah; Barbie, David; Gandhi, Leena; Lander, Eric S.; Gray, Stacy W.; Joffe, Steven; Janne, Pasi; Garber, Judy; MacConaill, Laura; Lindeman, Neal; Rollins, Barrett; Kantoff, Philip; Fisher, Sheila A.; Gabriel, Stacey; Getz, Gad; Garraway, Levi A. (2013)
      Translating whole exome sequencing (WES) for prospective clinical use may impact the care of cancer patients; however, multiple innovations are necessary for clinical implementation. These include: (1) rapid and robust WES ...