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2014
Response and acquired resistance to everolimus in anaplastic thyroid cancer.Wagle, N., Grabiner BC, Van Allen EM, Amin-Mansour A., Taylor-Weiner A., Rosenberg M., Gray N., Barletta JA, Guo Y., Swanson SJ, Ruan DT, Hanna GJ, Haddad RI, Getz G., Kwiatkowski DJ, Carter SL, Sabatini DM, Jänne PA, Garraway LA, and Lorch JH The New England journal of medicine, 2014/10/09, Volume 371, Issue 15, p.1426-33, (2014) Read More / View Supplemental Materials
Abstract
The Genomic Landscape of Pediatric Ewing Sarcoma.Crompton, BD, Stewart C., Taylor-Weiner A., Alexe G., Kurek KC, Calicchio ML, Kiezun A., Carter SL, Shukla SA, Mehta SS, Thorner AR, de Torres C., Lavarino C., Sunol M., McKenna A., Sivachenko A., Cibulskis K., Lawrence MS, Stojanov P., Rosenberg M., et al. Cancer discovery, 2014/09/03, (2014) Read More / View Supplemental Materials
Abstract
Computational pathology: an emerging definition.Louis, DN, Gerber GK, Baron JM, Bry L., Dighe AS, Getz G., Higgins JM, Kuo FC, Lane WJ, Michaelson JS, Le LP, Mermel CH, Gilbertson JR, and Golden JA Archives of pathology & laboratory medicine, 2014/09/01, Volume 138, Issue 9, p.1133-8, (2014) Read More / View Supplemental Materials
Somatic Mutations Predict Poor Outcome in Patients With Myelodysplastic Syndrome After Hematopoietic Stem-Cell Transplantation.Bejar, R., Stevenson KE, Caughey B., Lindsley RC, Mar BG, Stojanov P., Getz G., Steensma DP, Ritz J., Soiffer R., Antin JH, Alyea E., Armand P., Ho V., Koreth J., Neuberg D., Cutler CS, and Ebert BL Journal of clinical oncology : official journal of the American Society of Clinical Oncology, 2014/08/04, (2014) Read More / View Supplemental Materials
Abstract
Integrative and comparative genomic analysis of HPV-positive and HPV-negative head and neck squamous cell carcinomas.Seiwert, TY, Zuo Z., Keck MK, Khattri A., Pedamallu CS, Stricker TP, Brown CD, Pugh TJ, Stojanov P., Cho J., Lawrence M., Getz G., Bragelmann J., DeBoer R., Weichselbaum RR, Langerman A., Portugal LD, Blair EA, Stenson KM, Lingen MW, et al. Clinical cancer research : an official journal of the American Association for Cancer Research, 2014/07/23, (2014) Read More / View Supplemental Materials
Abstract
Cancer therapy. Ex vivo culture of circulating breast tumor cells for individualized testing of drug susceptibility.Yu, M., Bardia A., Aceto N., Bersani F., Madden MW, Donaldson MC, Desai R., Zhu H., Comaills V., Zheng Z., Wittner BS, Stojanov P., Brachtel E., Sgroi D., Kapur R., Shioda T., Ting DT, Ramaswamy S., Getz G., Iafrate AJ, et al. Science (New York, N.Y.), 2014/07/11, Volume 345, Issue 6193, p.216-20, (2014) Read More / View Supplemental Materials
Abstract
Assessing the clinical utility of cancer genomic and proteomic data across tumor types.Yuan, Y., Van Allen EM, Omberg L., Wagle N., Amin-Mansour A., Sokolov A., Byers LA, Xu Y., Hess KR, Diao L., Han L., Huang X., Lawrence MS, Weinstein J. N., Stuart JM, Mills GB, Garraway LA, Margolin AA, Getz G., and Liang H. Nature biotechnology, 2014/07/01, Volume 32, Issue 7, p.644-52, (2014) Read More / View Supplemental Materials
Abstract
Exome sequencing of pleuropulmonary blastoma reveals frequent biallelic loss of TP53 and two hits in DICER1 resulting in retention of 5p-derived miRNA hairpin loop sequences.Pugh, TJ, Yu W., Yang J., Field AL, Ambrogio L., Carter SL, Cibulskis K., Giannikopoulos P., Kiezun A., Kim J., McKenna A., Nickerson E., Getz G., Hoffher S., Messinger YH, Dehner LP, Roberts CW, Rodriguez-Galindo C., Williams GM, Rossi CT, et al. Oncogene, 2014/06/09, (2014) Read More / View Supplemental Materials
Abstract
Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia.Rajasagi, M., Shukla SA, Fritsch EF, Keskin DB, Deluca D., Carmona E., Zhang W., Sougnez C., Cibulskis K., Sidney J., Stevenson K., Ritz J., Neuberg D., Brusic V., Gabriel S., Lander E. S., Getz G., Hacohen N., and Wu CJ Blood, 2014/06/02, (2014) Read More / View Supplemental Materials
Abstract
Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine.Van Allen, EM, Wagle N., Stojanov P., Perrin DL, Cibulskis K., Marlow S., Jane-Valbuena J., Friedrich DC, Kryukov G., Carter SL, McKenna A., Sivachenko A., Rosenberg M., Kiezun A., Voet D., Lawrence M., Lichtenstein LT, Gentry JG, Huang FW, Fostel J., et al. Nature medicine, 2014/06/01, Volume 20, Issue 6, p.682-8, (2014) Read More / View Supplemental Materials
Abstract
Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing.Helman, E., Lawrence ML, Stewart C., Sougnez C., Getz G., and Meyerson M. Genome research, 2014/05/13, (2014) Read More / View Supplemental Materials
Abstract
Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer.Lohr, JG, Adalsteinsson VA, Cibulskis K., Choudhury AD, Rosenberg M., Cruz-Gordillo P., Francis JM, Zhang CZ, Shalek AK, Satija R., Trombetta JJ, Lu D., Tallapragada N., Tahirova N., Kim S., Blumenstiel B., Sougnez C., Lowe A., Wong B., Auclair D., et al. Nature biotechnology, 2014/05/01, Volume 32, Issue 5, p.479-84, (2014) Read More / View Supplemental Materials
Abstract
Somatic mutation as a mechanism of Wnt/β-catenin pathway activation in CLL.Wang, L., Shalek AK, Lawrence M., Ding R., Gaublomme JT, Pochet N., Stojanov P., Sougnez C., Shukla SA, Stevenson KE, Zhang W., Wong J., Sievers QL, Macdonald BT, Vartanov AR, Goldstein NR, Neuberg D., He X., Lander E., Hacohen N., et al. Blood, 2014/04/28, (2014) Read More / View Supplemental Materials
Abstract
PRADA: pipeline for RNA sequencing data analysis.Torres-García, W., Zheng S., Sivachenko A., Vegesna R., Wang Q., Yao R., Berger MF, Weinstein J. N., Getz G., and Verhaak RG Bioinformatics (Oxford, England), 2014/04/25, (2014) Read More / View Supplemental Materials
Abstract
Genetic and clonal dissection of murine small cell lung carcinoma progression by genome sequencing.McFadden, DG, Papagiannakopoulos T., Taylor-Weiner A., Stewart C., Carter SL, Cibulskis K., Bhutkar A., McKenna A., Dooley A., Vernon A., Sougnez C., Malstrom S., Heimann M., Park J., Chen F., Farago AF, Dayton T., Shefler E., Gabriel S., Getz G., et al. Cell, 2014/03/13, Volume 156, Issue 6, p.1298-311, (2014) Read More / View Supplemental Materials
Abstract
Exome sequencing identifies BRAF mutations in papillary craniopharyngiomas.Brastianos, PK, Taylor-Weiner A., Manley PE, Jones RT, Dias-Santagata D., Thorner AR, Lawrence MS, Rodriguez FJ, Bernardo LA, Schubert L., Sunkavalli A., Shillingford N., Calicchio ML, Lidov HG, Taha H., Martinez-Lage M., Santi M., Storm PB, Lee JY, Palmer JN, et al. Nature genetics, 2014/02/01, Volume 46, Issue 2, p.161-5, (2014) Read More / View Supplemental Materials
Abstract
In vivo multiplexed interrogation of amplified genes identifies GAB2 as an ovarian cancer oncogene.Dunn, GP, Cheung HW, Agarwalla PK, Thomas S., Zektser Y., Karst AM, Boehm JS, Weir BA, Berlin AM, Zou L., Getz G., Liu JF, Hirsch M., Vazquez F., Root DE, Beroukhim R., Drapkin R., and Hahn WC Proceedings of the National Academy of Sciences of the United States of America, 2014/01/21, Volume 111, Issue 3, p.1102-7, (2014) Read More / View Supplemental Materials
Abstract
Widespread genetic heterogeneity in multiple myeloma: implications for targeted therapy.Lohr, JG, Stojanov P., Carter SL, Cruz-Gordillo P., Lawrence MS, Auclair D., Sougnez C., Knoechel B., Gould J., Saksena G., Cibulskis K., McKenna A., Chapman MA, Straussman R., Levy J., Perkins LM, Keats JJ, Schumacher SE, Rosenberg M., Multiple Myeloma Research Consortium, et al. Cancer cell, 2014/01/13, Volume 25, Issue 1, p.91-101, (2014) Read More / View Supplemental Materials
Abstract
Discovery and saturation analysis of cancer genes across 21 tumour types.Lawrence, MS, Stojanov P., Mermel CH, Robinson JT, Garraway LA, Golub T. R., Meyerson M., Gabriel SB, Lander E. S., and Getz G. Nature, 2014/01/05, (2014) Read More / View Supplemental Materials
Abstract
A Pan-Cancer Analysis of Transcriptome Changes Associated with Somatic Mutations in U2AF1 Reveals Commonly Altered Splicing Events.Brooks, AN, Choi PS, de Waal L., Sharifnia T., Imielinski M., Saksena G., Pedamallu CS, Sivachenko A., Rosenberg M., Chmielecki J., Lawrence MS, Deluca DS, Getz G., and Meyerson M. PloS one, 2014/01/01, Volume 9, Issue 1, p.e87361, (2014) Read More / View Supplemental Materials
Abstract
2013
Landscape of genomic alterations in cervical carcinomas.Ojesina, AI, Lichtenstein L., Freeman SS, Pedamallu CS, Imaz-Rosshandler I., Pugh TJ, Cherniack AD, Ambrogio L., Cibulskis K., Bertelsen B., Romero-Cordoba S., Treviño V., Vazquez-Santillan K., Guadarrama AS, Wright AA, Rosenberg MW, Duke F., Kaplan B., Wang R., Nickerson E., et al. Nature, 2013/12/25, (2013) Read More / View Supplemental Materials
Abstract
Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair.Polak, P., Lawrence MS, Haugen E., Stoletzki N., Stojanov P., Thurman RE, Garraway LA, Mirkin S., Getz G., Stamatoyannopoulos JA, and Sunyaev SR Nature biotechnology, 2013/12/15, (2013) Read More / View Supplemental Materials
Abstract
Integrative and Comparative Genomic Analysis of Lung Squamous Cell Carcinomas in East Asian Patients.Kim, Y., Hammerman PS, Kim J., Yoon JA, Lee Y., Sun JM, Wilkerson MD, Pedamallu CS, Cibulskis K., Yoo YK, Lawrence MS, Stojanov P., Carter SL, McKenna A., Stewart C., Sivachenko AY, Oh IJ, Kim HK, Choi YS, Kim K., et al. Journal of clinical oncology : official journal of the American Society of Clinical Oncology, 2013/12/09, (2013) Read More / View Supplemental Materials
Abstract
Somatic mutation of CDKN1B in small intestine neuroendocrine tumors.Francis, JM, Kiezun A., Ramos AH, Serra S., Pedamallu CS, Qian ZR, Banck MS, Kanwar R., Kulkarni AA, Karpathakis A., Manzo V., Contractor T., Philips J., Nickerson E., Pho N., Hooshmand SM, Brais LK, Lawrence MS, Pugh T., McKenna A., et al. Nature genetics, 2013/12/01, Volume 45, Issue 12, p.1483-6, (2013) Read More / View Supplemental Materials
Abstract
The somatic genomic landscape of glioblastoma.Brennan, CW, Verhaak RG, McKenna A., Campos B., Noushmehr H., Salama SR, Zheng S., Chakravarty D., Sanborn JZ, Berman SH, Beroukhim R., Bernard B., Wu CJ, Genovese G., Shmulevich I., Barnholtz-Sloan J., Zou L., Vegesna R., Shukla SA, Ciriello G., et al. Cell, 2013/10/10, Volume 155, Issue 2, p.462-77, (2013) Read More / View Supplemental Materials
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Comprehensive identification of mutational cancer driver genes across 12 tumor types.Tamborero, D., Gonzalez-Perez A., Perez-Llamas C., Deu-Pons J., Kandoth C., Reimand J., Lawrence MS, Getz G., Bader GD, Ding L., and Lopez-Bigas N. Scientific reports, 2013/10/02, Volume 3, p.2650, (2013) Read More / View Supplemental Materials
Abstract
The Cancer Genome Atlas Pan-Cancer analysis project.Cancer Genome Atlas Research, Network, Genome Characterization Center, Chang K., Creighton CJ, Davis C., Donehower L., Drummond J., Wheeler D., Ally A., Balasundaram M., Birol I., Butterfield YS, Chu A., Chuah E., Chun HJ, Dhalla N., Guin R., Hirst M., Hirst C., Holt RA, et al. Nature genetics, 2013/09/26, Volume 45, Issue 10, p.1113-20, (2013) Read More / View Supplemental Materials
Pan-cancer patterns of somatic copy number alteration.Zack, TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G., Tabak B., Lawrence MS, Zhang CZ, Wala J., Mermel CH, Sougnez C., Gabriel SB, Hernandez B., Shen H., Laird PW, Getz G., Meyerson M., and Beroukhim R. Nature genetics, 2013/09/26, Volume 45, Issue 10, p.1134-1140, (2013) Read More / View Supplemental Materials
Abstract
An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers.Roberts, SA, Lawrence MS, Klimczak LJ, Grimm SA, Fargo D., Stojanov P., Kiezun A., Kryukov GV, Carter SL, Saksena G., Harris S., Shah RR, Resnick MA, Getz G., and Gordenin DA Nature genetics, 2013/08/28, Volume 45, Issue 9, p.970-6, (2013) Read More / View Supplemental Materials
Abstract
Clonal evolution in hematological malignancies and therapeutic implications.Landau, DA, Carter SL, Getz G., and Wu CJ Leukemia, 2013/08/27, (2013) Read More / View Supplemental Materials
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Mutational heterogeneity in cancer and the search for new cancer-associated genes.Lawrence, MS, Stojanov P., Polak P., Kryukov GV, Cibulskis K., Sivachenko A., Carter SL, Stewart C., Mermel CH, Roberts SA, Kiezun A., Hammerman PS, McKenna A., Drier Y., Zou L., Ramos AH, Pugh TJ, Stransky N., Helman E., Kim J., et al. Nature, 2013/07/11, Volume 499, Issue 7457, p.214-8, (2013) Read More / View Supplemental Materials
Abstract
Comprehensive molecular characterization of clear cell renal cell carcinoma.The Cancer Genome Atlas Research, Network, Analysis working group: Baylor College of Medicine, Creighton CJ, Morgan M., Gunaratne PH, Wheeler DA, Gibbs RA, BC Cancer Agency, Gordon Robertson A., Chu A., Broad Institute, Beroukhim R., Cibulskis K., Brigham & Women’s Hospital, Signoretti S., Brown University, Vandin Hsin-Ta Wu F., Raphael BJ, The University of Texas MD Anderson Cancer Center, Verhaak RG, et al. Nature, 2013/06/23, (2013) Read More / View Supplemental Materials
Abstract
Inhibitor-sensitive FGFR2 and FGFR3 mutations in lung squamous cell carcinoma.Liao, RG, Jung J., Tchaicha JH, Wilkerson MD, Sivachenko A., Beauchamp EM, Pugh TJ, Pedamallu CS, Hayes DN, Gray NS, Getz G., Wong KK, Meyerson M., and Hammerman PS Cancer research, 2013/06/20, (2013) Read More / View Supplemental Materials
Abstract
Mutations in isocitrate dehydrogenase 1 and 2 occur frequently in intrahepatic cholangiocarcinomas and share hypermethylation targets with glioblastomas.Wang, P., Dong Q., Zhang C., Kuan PF, Liu Y., Jeck WR, Andersen JB, Jiang W., Savich GL, Tan TX, Auman JT, Hoskins JM, Misher AD, Moser CD, Yourstone SM, Kim JW, Cibulskis K., Getz G., Hunt HV, Thorgeirsson SS, et al. Oncogene, 2013/06/20, Volume 32, Issue 25, p.3091-100, (2013) Read More / View Supplemental Materials
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The Genotype-Tissue Expression (GTEx) project.Lonsdale, J., Thomas J., Salvatore M., Phillips R., Lo E., Shad S., Hasz R., Walters G., Garcia F., Young N., Foster B., Moser M., Karasik E., Gillard B., Ramsey K., Sullivan S., Bridge J., Magazine H., Syron J., Fleming J., et al. Nature genetics, 2013/05/29, Volume 45, Issue 6, p.580-5, (2013) Read More / View Supplemental Materials
Genomic analysis of diffuse pediatric low-grade gliomas identifies recurrent oncogenic truncating rearrangements in the transcription factor MYBL1.Ramkissoon, LA, Horowitz PM, Craig JM, Ramkissoon SH, Rich BE, Schumacher SE, McKenna A., Lawrence MS, Bergthold G., Brastianos PK, Tabak B., Ducar MD, Van Hummelen P., Macconaill LE, Pouissant-Young T., Cho YJ, Taha H., Mahmoud M., Bowers DC, Margraf L., et al. Proceedings of the National Academy of Sciences of the United States of America, 2013/05/14, Volume 110, Issue 20, p.8188-93, (2013) Read More / View Supplemental Materials
Abstract
Integrated genomic characterization of endometrial carcinoma.Cancer Genome Atlas Research, Network, Genome sequencing centres: Broad Institute, Getz G., Gabriel SB, Cibulskis K., Lander E., Sivachenko A., Sougnez C., Lawrence M., Washington University in St Louis, Kandoth C., Dooling D., Fulton R., Fulton L., Kalicki-Veizer J., McLellan MD, O'Laughlin M., Schmidt H., Wilson RK, Ye K., et al. Nature, 2013/05/02, Volume 497, Issue 7447, p.67-73, (2013) Read More / View Supplemental Materials
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Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity.Dulak, AM, Stojanov P., Peng S., Lawrence MS, Fox C., Stewart C., Bandla S., Imamura Y., Schumacher SE, Shefler E., McKenna A., Carter SL, Cibulskis K., Sivachenko A., Saksena G., Voet D., Ramos AH, Auclair D., Thompson K., Sougnez C., et al. Nature genetics, 2013/04/26, Volume 45, Issue 5, p.478-86, (2013) Read More / View Supplemental Materials
Abstract
Punctuated evolution of prostate cancer genomes.Baca, SC, Prandi D., Lawrence MS, Mosquera JM, Romanel A., Drier Y., Park K., Kitabayashi N., MacDonald TY, Ghandi M., Van Allen E., Kryukov GV, Sboner A., Theurillat JP, Soong TD, Nickerson E., Auclair D., Tewari A., Beltran H., Onofrio RC, et al. Cell, 2013/04/25, Volume 153, Issue 3, p.666-77, (2013) Read More / View Supplemental Materials
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Nozzle: a report generation toolkit for data analysis pipelines.Gehlenborg, N., Noble MS, Getz G., Chin L., and Park PJ Bioinformatics (Oxford, England), 2013/03/11, (2013) Read More / View Supplemental Materials
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Evolution and impact of subclonal mutations in chronic lymphocytic leukemia.Landau, DA, Carter SL, Stojanov P., McKenna A., Stevenson K., Lawrence MS, Sougnez C., Stewart C., Sivachenko A., Wang L., Wan Y., Zhang W., Shukla SA, Vartanov A., Fernandes SM, Saksena G., Cibulskis K., Tesar B., Gabriel S., Hacohen N., et al. Cell, 2013/02/14, Volume 152, Issue 4, p.714-26, (2013) Read More / View Supplemental Materials
Abstract
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples.Cibulskis, K., Lawrence MS, Carter SL, Sivachenko A., Jaffe D., Sougnez C., Gabriel S., Meyerson M., Lander E. S., and Getz G. Nature biotechnology, 2013/02/10, (2013) Read More / View Supplemental Materials
Abstract
The genetic landscape of high-risk neuroblastoma.Pugh, TJ, Morozova O., Attiyeh EF, Asgharzadeh S., Wei JS, Auclair D., Carter SL, Cibulskis K., Hanna M., Kiezun A., Kim J., Lawrence MS, McKenna A., Pedamallu CS, Ramos AH, Shefler E., Sivachenko A., Sougnez C., Stewart C., Ally A., et al. Nature genetics, 2013/01/20, (2013) Read More / View Supplemental Materials
Abstract
Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations.Brastianos, PK, Horowitz PM, Santagata S., Jones RT, McKenna A., Getz G., Ligon KL, Palescandolo E., Van Hummelen P., Ducar MD, Raza A., Macconaill LE, Louis DN, Hahn WC, Dunn IF, and Beroukhim R. Nature genetics, 2013/01/20, (2013) Read More / View Supplemental Materials
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Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation.Costello, M., Pugh TJ, Fennell TJ, Stewart C., Lichtenstein L., Meldrim JC, Fostel JL, Friedrich DC, Perrin D., Dionne D., Kim S., Gabriel SB, Lander E. S., Fisher S., and Getz G. Nucleic acids research, 2013/01/08, (2013) Read More / View Supplemental Materials
Abstract
2012
Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.Barretina, J., Caponigro G., Stransky N., Venkatesan K., Margolin AA, Kim S., Wilson CJ, Lehár J., Kryukov GV, Sonkin D., Reddy A., Liu M., Murray L., Berger MF, Monahan JE, Morais P., Meltzer J., Korejwa A., Jané-Valbuena J., Mapa FA, et al. Nature, 2012/12/13, Volume 492, Issue 7428, p.290, (2012) Read More / View Supplemental Materials
Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability.Drier, Y., Lawrence MS, Carter SL, Stewart C., Gabriel SB, Lander E. S., Meyerson M., Beroukhim R., and Getz G. Genome research, 2012/11/02, (2012) Read More / View Supplemental Materials
Abstract
Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing.Imielinski, M., Berger AH, Hammerman PS, Hernandez B., Pugh TJ, Hodis E., Cho J., Sivachenko A., Sougnez C., Auclair D., Lawrence MS, Stojanov P., Cibulskis K., Sharifnia T., Greulich H., Banerji S., Zander T., Thompson K., Winckler W., Kwiatkowski D., et al. Cell, 2012/09/14, Volume 150, Issue 6, p.1107-20, (2012) Read More / View Supplemental Materials
Abstract
Integrative Analysis Reveals an Outcome-Associated and Targetable Pattern of p53 and Cell Cycle Deregulation in Diffuse Large B Cell Lymphoma.Monti, S., Chapuy B., Takeyama K., Rodig SJ, Hao Y., Yeda KT, Inguilizian H., Mermel C., Currie T., Dogan A., Kutok JL, Beroukhim R., Neuberg D., Habermann TM, Getz G., Kung AL, Golub T. R., and Shipp M. A. Cancer cell, 2012/09/11, Volume 22, Issue 3, p.359-72, (2012) Read More / View Supplemental Materials
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Comprehensive genomic characterization of squamous cell lung cancers.The Cancer Genome Atlas Research, Network, institution.)(Participants are arranged by area of contribution and then by, Genome sequencing centres: Broad Institute, Hammerman PS, Lawrence MS, Voet D., Jing R., Cibulskis K., Sivachenko A., Stojanov P., McKenna A., Lander E. S., Gabriel S., Getz G., Sougnez C., Imielinski M., Helman E., Hernandez B., Pho NH, Meyerson M., et al. Nature, 2012/09/09, (2012) Read More / View Supplemental Materials
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Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2.Greulich, H., Kaplan B., Mertins P., Chen TH, Tanaka KE, Yun CH, Zhang X., Lee SH, Cho J., Ambrogio L., Liao R., Imielinski M., Banerji S., Berger AH, Lawrence MS, Zhang J., Pho NH, Walker SR, Winckler W., Getz G., et al. Proceedings of the National Academy of Sciences of the United States of America, 2012/09/04, Volume 109, Issue 36, p.14476-81, (2012) Read More / View Supplemental Materials
Abstract
Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations.Pugh, TJ, Weeraratne SD, Archer TC, Pomeranz Krummel DA, Auclair D., Bochicchio J., Carneiro MO, Carter SL, Cibulskis K., Erlich RL, Greulich H., Lawrence MS, Lennon NJ, McKenna A., Meldrim J., Ramos AH, Ross MG, Russ C., Shefler E., Sivachenko A., et al. Nature, 2012/08/02, Volume 488, Issue 7409, p.106-10, (2012) Read More / View Supplemental Materials
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A landscape of driver mutations in melanoma.Hodis, E., Watson IR, Kryukov GV, Arold ST, Imielinski M., Theurillat JP, Nickerson E., Auclair D., Li L., Place C., Dicara D., Ramos AH, Lawrence MS, Cibulskis K., Sivachenko A., Voet D., Saksena G., Stransky N., Onofrio RC, Winckler W., et al. Cell, 2012/07/20, Volume 150, Issue 2, p.251-63, (2012) Read More / View Supplemental Materials
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Paired-end sequencing of Fosmid libraries by Illumina.Williams, LJ, Tabbaa DG, Li N., Berlin AM, Shea TP, Maccallum I., Lawrence MS, Drier Y., Getz G., Young SK, Jaffe DB, Nusbaum C., and Gnirke A. Genome research, 2012/07/17, (2012) Read More / View Supplemental Materials
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A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers.Lee, RS, Stewart C., Carter SL, Ambrogio L., Cibulskis K., Sougnez C., Lawrence MS, Auclair D., Mora J., Golub T. R., Biegel JA, Getz G., and Roberts CW The Journal of clinical investigation, 2012/07/16, (2012) Read More / View Supplemental Materials
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Sequence analysis of mutations and translocations across breast cancer subtypes.Banerji, S., Cibulskis K., Rangel-Escareno C., Brown KK, Carter SL, Frederick AM, Lawrence MS, Sivachenko AY, Sougnez C., Zou L., Cortes ML, Fernandez-Lopez JC, Peng S., Ardlie KG, Auclair D., Bautista-Piña V., Duke F., Francis J., Jung J., Maffuz-Aziz A., et al. Nature, 2012/06/20, Volume 486, Issue 7403, p.405-9, (2012) Read More / View Supplemental Materials
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RNA-SeQC: RNA-seq metrics for quality control and process optimization.Deluca, DS, Levin JZ, Sivachenko A., Fennell T., Nazaire MD, Williams C., Reich M., Winckler W., and Getz G. Bioinformatics (Oxford, England), 2012/06/01, Volume 28, Issue 11, p.1530-2, (2012) Read More / View Supplemental Materials
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Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer.Barbieri, CE, Baca SC, Lawrence MS, Demichelis F., Blattner M., Theurillat JP, White TA, Stojanov P., Van Allen E., Stransky N., Nickerson E., Chae SS, Boysen G., Auclair D., Onofrio RC, Park K., Kitabayashi N., MacDonald TY, Sheikh K., Vuong T., et al. Nature genetics, 2012/05/20, Volume 44, Issue 6, p.685-9, (2012) Read More / View Supplemental Materials
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Melanoma genome sequencing reveals frequent PREX2 mutations.Berger, MF, Hodis E., Heffernan TP, Deribe YL, Lawrence MS, Protopopov A., Ivanova E., Watson IR, Nickerson E., Ghosh P., Zhang H., Zeid R., Ren X., Cibulskis K., Sivachenko AY, Wagle N., Sucker A., Sougnez C., Onofrio R., Ambrogio L., et al. Nature, 2012/05/09, Volume 485, Issue 7399, p.502-6, (2012) Read More / View Supplemental Materials
Abstract
Absolute quantification of somatic DNA alterations in human cancer.Carter, SL, Cibulskis K., Helman E., McKenna A., Shen H., Zack T., Laird PW, Onofrio RC, Winckler W., Weir BA, Beroukhim R., Pellman D., Levine DA, Lander E. S., Meyerson M., and Getz G. Nature biotechnology, 2012/04/29, (2012) Read More / View Supplemental Materials
Abstract
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.Barretina, J., Caponigro G., Stransky N., Venkatesan K., Margolin AA, Kim S., Wilson CJ, Lehár J., Kryukov GV, Sonkin D., Reddy A., Liu M., Murray L., Berger MF, Monahan JE, Morais P., Meltzer J., Korejwa A., Jané-Valbuena J., Mapa FA, et al. Nature, 2012/03/28, Volume 483, Issue 7391, p.603-7, (2012) Read More / View Supplemental Materials
Abstract
Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing.Lohr, JG, Stojanov P., Lawrence MS, Auclair D., Chapuy B., Sougnez C., Cruz-Gordillo P., Knoechel B., Asmann YW, Slager SL, Novak AJ, Dogan A., Ansell SM, Link BK, Zou L., Gould J., Saksena G., Stransky N., Rangel-Escareño C., Fernandez-Lopez JC, et al. Proceedings of the National Academy of Sciences of the United States of America, 2012/03/06, Volume 109, Issue 10, p.3879-84, (2012) Read More / View Supplemental Materials
Abstract
GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.Mermel, CH, Schumacher SE, Hill B., Meyerson ML, Beroukhim R., and Getz G. Genome biology, 2012/01/09, Volume 12, Issue 4, p.R41, (2012) Read More / View Supplemental Materials
Abstract
2011
SF3B1 and other novel cancer genes in chronic lymphocytic leukemia.Wang, L., Lawrence MS, Wan Y., Stojanov P., Sougnez C., Stevenson K., Werner L., Sivachenko A., Deluca DS, Zhang L., Zhang W., Vartanov AR, Fernandes SM, Goldstein NR, Folco EG, Cibulskis K., Tesar B., Sievers QL, Shefler E., Gabriel S., et al. The New England journal of medicine, 2011/12/29, Volume 365, Issue 26, p.2497-506, (2011) Read More / View Supplemental Materials
Abstract
ContEst: estimating cross-contamination of human samples in next-generation sequencing data.Cibulskis, K., McKenna A., Fennell T., Banks E., DePristo M., and Getz G. Bioinformatics (Oxford, England), 2011/09/15, Volume 27, Issue 18, p.2601-2, (2011) Read More / View Supplemental Materials
Abstract
Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion.Bass, AJ, Lawrence MS, Brace LE, Ramos AH, Drier Y., Cibulskis K., Sougnez C., Voet D., Saksena G., Sivachenko A., Jing R., Parkin M., Pugh T., Verhaak RG, Stransky N., Boutin AT, Barretina J., Solit DB, Vakiani E., Shao W., et al. Nature genetics, 2011/09/04, Volume 43, Issue 10, p.964-8, (2011) Read More / View Supplemental Materials
Abstract
The mutational landscape of head and neck squamous cell carcinoma.Stransky, N., Egloff AM, Tward AD, Kostic AD, Cibulskis K., Sivachenko A., Kryukov GV, Lawrence MS, Sougnez C., McKenna A., Shefler E., Ramos AH, Stojanov P., Carter SL, Voet D., Cortés ML, Auclair D., Berger MF, Saksena G., Guiducci C., et al. Science (New York, N.Y.), 2011/08/26, Volume 333, Issue 6046, p.1157-60, (2011) Read More / View Supplemental Materials
Abstract
Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer.Cheung, HW, Cowley GS, Weir BA, Boehm JS, Rusin S., Scott JA, East A., Ali LD, Lizotte PH, Wong TC, Jiang G., Hsiao J., Mermel CH, Getz G., Barretina J., Gopal S., Tamayo P., Gould J., Tsherniak A., Stransky N., et al. Proceedings of the National Academy of Sciences of the United States of America, 2011/07/26, Volume 108, Issue 30, p.12372-7, (2011) Read More / View Supplemental Materials
Abstract
Initial genome sequencing and analysis of multiple myeloma.Chapman, MA, Lawrence MS, Keats JJ, Cibulskis K., Sougnez C., Schinzel AC, Harview CL, Brunet JP, Ahmann GJ, Adli M., Anderson KC, Ardlie KG, Auclair D., Baker A., Bergsagel PL, Bernstein BE, Drier Y., Fonseca R., Gabriel SB, Hofmeister CC, et al. Nature, 2011/03/24, Volume 471, Issue 7339, p.467-72, (2011) Read More / View Supplemental Materials
Abstract
The genomic complexity of primary human prostate cancer.Berger, MF, Lawrence MS, Demichelis F., Drier Y., Cibulskis K., Sivachenko AY, Sboner A., Esgueva R., Pflueger D., Sougnez C., Onofrio R., Carter SL, Park K., Habegger L., Ambrogio L., Fennell T., Parkin M., Saksena G., Voet D., Ramos AH, et al. Nature, 2011/02/10, Volume 470, Issue 7333, p.214-20, (2011) Read More / View Supplemental Materials
Abstract
Integrative genomics viewer.Robinson, JT, Thorvaldsdóttir H., Winckler W., Guttman M., Lander E. S., Getz G., and Mesirov J. P. Nature biotechnology, 2011/01/01, Volume 29, Issue 1, p.24-6, (2011) Read More / View Supplemental Materials
2010
Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy.Barretina, J., Taylor BS, Banerji S., Ramos AH, Lagos-Quintana M., Decarolis PL, Shah K., Socci ND, Weir BA, Ho A., Chiang DY, Reva B., Mermel CH, Getz G., Antipin Y., Beroukhim R., Major JE, Hatton C., Nicoletti R., Hanna M., et al. Nature genetics, 2010/08/01, Volume 42, Issue 8, p.715-21, (2010) Read More / View Supplemental Materials
Abstract
International network of cancer genome projects.International Cancer Genome, Consortium, Hudson T. J., Anderson W., Artez A., Barker AD, Bell C., Bernabé RR, Bhan MK, Calvo F., Eerola I., Gerhard DS, Guttmacher A., Guyer M., Hemsley FM, Jennings JL, Kerr D., Klatt P., Kolar P., Kusada J., Lane DP, et al. Nature, 2010/04/15, Volume 464, Issue 7291, p.993-8, (2010) Read More / View Supplemental Materials
Abstract
Integrative analysis of the melanoma transcriptome.Berger, MF, Levin JZ, Vijayendran K., Sivachenko A., Adiconis X., Maguire J., Johnson LA, Robinson J., Verhaak RG, Sougnez C., Onofrio RC, Ziaugra L., Cibulskis K., Laine E., Barretina J., Winckler W., Fisher DE, Getz G., Meyerson M., Jaffe DB, et al. Genome research, 2010/04/01, Volume 20, Issue 4, p.413-27, (2010) Read More / View Supplemental Materials
Abstract
The landscape of somatic copy-number alteration across human cancers.Beroukhim, R., Mermel CH, Porter D., Wei G., Raychaudhuri S., Donovan J., Barretina J., Boehm JS, Dobson J., Urashima M., Mc Henry KT, Pinchback RM, Ligon AH, Cho YJ, Haery L., Greulich H., Reich M., Winckler W., Lawrence MS, Weir BA, et al. Nature, 2010/02/18, Volume 463, Issue 7283, p.899-905, (2010) Read More / View Supplemental Materials
Abstract
Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1.Verhaak, RG, Hoadley KA, Purdom E., Wang V., Qi Y., Wilkerson MD, Miller CR, Ding L., Golub T., Mesirov J. P., Alexe G., Lawrence M., O'Kelly M., Tamayo P., Weir BA, Gabriel S., Winckler W., Gupta S., Jakkula L., Feiler HS, et al. Cancer cell, 2010/01/19, Volume 17, Issue 1, p.98-110, (2010) Read More / View Supplemental Materials
Abstract
2009
Integrated genomic profiling of endometrial carcinoma associates aggressive tumors with indicators of PI3 kinase activation.Salvesen, HB, Carter SL, Mannelqvist M., Dutt A., Getz G., Stefansson IM, Raeder MB, Sos ML, Engelsen IB, Trovik J., Wik E., Greulich H., Bø TH, Jonassen I., Thomas RK, Zander T., Garraway LA, Oyan AM, Sellers WR, Kalland KH, et al. Proceedings of the National Academy of Sciences of the United States of America, 2009/03/24, Volume 106, Issue 12, p.4834-9, (2009) Read More / View Supplemental Materials
Abstract
High-resolution mapping of copy-number alterations with massively parallel sequencing.Chiang, DY, Getz G., Jaffe DB, O'Kelly MJ, Zhao X., Carter SL, Russ C., Nusbaum C., Meyerson M., and Lander E. S. Nature methods, 2009/01/01, Volume 6, Issue 1, p.99-103, (2009) Read More / View Supplemental Materials
Abstract
2008
Somatic mutations affect key pathways in lung adenocarcinoma.Ding, L., Getz G., Wheeler DA, Mardis ER, McLellan MD, Cibulskis K., Sougnez C., Greulich H., Muzny DM, Morgan MB, Fulton L., Fulton RS, Zhang Q., Wendl MC, Lawrence MS, Larson DE, Chen K., Dooling DJ, Sabo A., Hawes AC, et al. Nature, 2008/10/23, Volume 455, Issue 7216, p.1069-75, (2008) Read More / View Supplemental Materials
Abstract
Modeling genomic diversity and tumor dependency in malignant melanoma.Lin, WM, Baker AC, Beroukhim R., Winckler W., Feng W., Marmion JM, Laine E., Greulich H., Tseng H., Gates C., Hodi FS, Dranoff G., Sellers WR, Thomas RK, Meyerson M., Golub T. R., Dummer R., Herlyn M., Getz G., and Garraway LA Cancer research, 2008/02/01, Volume 68, Issue 3, p.664-73, (2008) Read More / View Supplemental Materials
Abstract
Integrative analysis reveals 53BP1 copy loss and decreased expression in a subset of human diffuse large B-cell lymphomasTakeyama, K., Monti S., Manis J. P., Cin Dal P., Getz G., Beroukhim R., Dutt S., Aster J. C., Alt F. W., Golub T. R., and Shipp M. A. Oncogene, 2008/01/10/, Volume 27, Issue 3, p.318 - 22, (2008) Read More / View Supplemental Materials
Abstract
2007
Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma.Beroukhim, R., Getz G., Nghiemphu L., Barretina J., Hsueh T., Linhart D., Vivanco I., Lee JC, Huang JH, Alexander S., Du J., Kau T., Thomas RK, Shah K., Soto H., Perner S., Prensner J., Debiasi RM, Demichelis F., Hatton C., et al. Proceedings of the National Academy of Sciences of the United States of America, 2007/12/11, Volume 104, Issue 50, p.20007-12, (2007) Read More / View Supplemental Materials
Abstract
Characterizing the cancer genome in lung adenocarcinoma.Weir, BA, Woo MS, Getz G., Perner S., Ding L., Beroukhim R., Lin WM, Province MA, Kraja A., Johnson LA, Shah K., Sato M., Thomas RK, Barletta JA, Borecki IB, Broderick S., Chang AC, Chiang DY, Chirieac LR, Cho J., et al. Nature, 2007/12/06, Volume 450, Issue 7171, p.893-8, (2007) Read More / View Supplemental Materials
Abstract
Comment on "The consensus coding sequences of human breast and colorectal cancers".Getz, G., Höfling H., Mesirov J. P., Golub T. R., Meyerson M., Tibshirani R., and Lander E. S. Science (New York, N.Y.), 2007/09/14, Volume 317, Issue 5844, p.1500, (2007) Read More / View Supplemental Materials
Abstract
2006
Epidermal growth factor receptor activation in glioblastoma through novel missense mutations in the extracellular domain.Lee, JC, Vivanco I., Beroukhim R., Huang JH, Feng WL, Debiasi RM, Yoshimoto K., King JC, Nghiemphu P., Yuza Y., Xu Q., Greulich H., Thomas RK, Paez JG, Peck TC, Linhart DJ, Glatt KA, Getz G., Onofrio R., Ziaugra L., et al. PLoS medicine, 2006/12/01, Volume 3, Issue 12, p.e485, (2006) Read More / View Supplemental Materials
Abstract
Comparative gene marker selection suite.Gould, J., Getz G., Monti S., Reich M., and Mesirov J. P. Bioinformatics (Oxford, England), 2006/08/01, Volume 22, Issue 15, p.1924-5, (2006) Read More / View Supplemental Materials
Abstract
BRAF mutation predicts sensitivity to MEK inhibition.Solit, DB, Garraway LA, Pratilas CA, Sawai A., Getz G., Basso A., Ye Q., Lobo JM, She Y., Osman I., Golub T. R., Sebolt-Leopold J., Sellers WR, and Rosen N. Nature, 2006/01/19, Volume 439, Issue 7074, p.358-62, (2006) Read More / View Supplemental Materials
Abstract
2005
Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma.Garraway, LA, Widlund HR, Rubin MA, Getz G., Berger AJ, Ramaswamy S., Beroukhim R., Milner DA, Granter SR, Du J., Lee C., Wagner SN, Li C., Golub T. R., Rimm DL, Meyerson ML, Fisher DE, and Sellers WR Nature, 2005/07/07, Volume 436, Issue 7047, p.117-22, (2005) Read More / View Supplemental Materials
Abstract
MicroRNA expression profiles classify human cancers.Lu, J., Getz G., Miska EA, Alvarez-Saavedra E., Lamb J., Peck D., Sweet-Cordero A., Ebert BL, Mak RH, Ferrando AA, Downing J. R., Jacks T., Horvitz HR, and Golub T. R. Nature, 2005/06/09, Volume 435, Issue 7043, p.834-8, (2005) Read More / View Supplemental Materials
Abstract
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