Search Results - "Berger, Ashton C."

Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma by Braun, David A., Hou, Yue, Bakouny, Ziad, Ficial, Miriam, Sant’ Angelo, Miriam, Forman, Juliet, Ross-Macdonald, Petra, Berger, Ashton C., Jegede, Opeyemi A., Elagina, Liudmilla, Steinharter, John, Sun, Maxine, Wind-Rotolo, Megan, Pignon, Jean-Christophe, Cherniack, Andrew D., Lichtenstein, Lee, Neuberg, Donna, Catalano, Paul, Freeman, Gordon J., Sharpe, Arlene H., McDermott, David F., Van Allen, Eliezer M., Signoretti, Sabina, Wu, Catherine J., Shukla, Sachet A., Choueiri, Toni K.

“…PD-1 blockade has transformed the management of advanced clear cell renal cell carcinoma (ccRCC), but the drivers and resistors of the PD-1 response remain…”
Get full text

Identification of ADAR1 adenosine deaminase dependency in a subset of cancer cells by Gannon, Hugh S., Zou, Tao, Kiessling, Michael K., Gao, Galen F., Cai, Diana, Choi, Peter S., Ivan, Alexandru P., Buchumenski, Ilana, Berger, Ashton C., Goldstein, Jonathan T., Cherniack, Andrew D., Vazquez, Francisca, Tsherniak, Aviad, Levanon, Erez Y., Hahn, William C., Meyerson, Matthew

“…Systematic exploration of cancer cell vulnerabilities can inform the development of novel cancer therapeutics. Here, through analysis of genome-scale…”
Get full text

Genomic and immune profiling of pre-invasive lung adenocarcinoma by Chen, Haiquan, Carrot-Zhang, Jian, Zhao, Yue, Hu, Haichuan, Freeman, Samuel S., Yu, Su, Ha, Gavin, Taylor, Alison M., Berger, Ashton C., Westlake, Lindsay, Zheng, Yuanting, Zhang, Jiyang, Ramachandran, Aruna, Zheng, Qiang, Pan, Yunjian, Zheng, Difan, Zheng, Shanbo, Cheng, Chao, Kuang, Muyu, Zhou, Xiaoyan, Zhang, Yang, Li, Hang, Ye, Ting, Ma, Yuan, Gao, Zhendong, Tao, Xiaoting, Han, Han, Shang, Jun, Yu, Ying, Bao, Ding, Huang, Yechao, Li, Xiangnan, Zhang, Yawei, Xiang, Jiaqing, Sun, Yihua, Li, Yuan, Cherniack, Andrew D., Campbell, Joshua D., Shi, Leming, Meyerson, Matthew

“…Adenocarcinoma in situ and minimally invasive adenocarcinoma are the pre-invasive forms of lung adenocarcinoma. The genomic and immune profiles of these…”
Get full text

Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities by Nichols, Caitlin A., Gibson, William J., Brown, Meredith S., Kosmicki, Jack A., Busanovich, John P., Wei, Hope, Urbanski, Laura M., Curimjee, Naomi, Berger, Ashton C., Gao, Galen F., Cherniack, Andrew D., Dhe-Paganon, Sirano, Paolella, Brenton R., Beroukhim, Rameen

“…Alterations in non-driver genes represent an emerging class of potential therapeutic targets in cancer. Hundreds to thousands of non-driver genes undergo loss…”
Get full text

Cancer aneuploidies are shaped primarily by effects on tumour fitness by Shih, Juliann, Sarmashghi, Shahab, Zhakula-Kostadinova, Nadja, Zhang, Shu, Georgis, Yohanna, Hoyt, Stephanie H., Cuoco, Michael S., Gao, Galen F., Spurr, Liam F., Berger, Ashton C., Ha, Gavin, Rendo, Veronica, Shen, Hui, Meyerson, Matthew, Cherniack, Andrew D., Taylor, Alison M., Beroukhim, Rameen

“…Aneuploidies—whole-chromosome or whole-arm imbalances—are the most prevalent alteration in cancer genomes 1 , 2 . However, it is still debated whether their…”
Get full text

Somatic Superenhancer Duplications and Hotspot Mutations Lead to Oncogenic Activation of the KLF5 Transcription Factor by Zhang, Xiaoyang, Choi, Peter S, Francis, Joshua M, Gao, Galen F, Campbell, Joshua D, Ramachandran, Aruna, Mitsuishi, Yoichiro, Ha, Gavin, Shih, Juliann, Vazquez, Francisca, Tsherniak, Aviad, Taylor, Alison M, Zhou, Jin, Wu, Zhong, Berger, Ashton C, Giannakis, Marios, Hahn, William C, Cherniack, Andrew D, Meyerson, Matthew

“…The Krüppel-like family of transcription factors plays critical roles in human development and is associated with cancer pathogenesis. Krüppel-like factor 5…”
Get more information

Author Correction: Identification of ADAR1 adenosine deaminase dependency in a subset of cancer cells by Gannon, Hugh S., Zou, Tao, Kiessling, Michael K., Gao, Galen F., Cai, Diana, Choi, Peter S., Ivan, Alexandru P., Buchumenski, Ilana, Berger, Ashton C., Goldstein, Jonathan T., Cherniack, Andrew D., Vazquez, Francisca, Tsherniak, Aviad, Levanon, Erez Y., Hahn, William C., Meyerson, Matthew

Get full text

Prognostic and therapeutic implications of tumor-restrictive type III collagen in the breast cancer microenvironment by Stewart, Daniel C., Brisson, Becky K., Dekky, Bassil, Berger, Ashton C., Yen, William, Mauldin, Elizabeth A., Loebel, Claudia, Gillette, Deborah, Assenmacher, Charles-Antoine, Quincey, Corisa, Stefanovski, Darko, Cristofanilli, Massimo, Cukierman, Edna, Burdick, Jason A., Borges, Virginia F., Volk, Susan W.

“…Collagen plays a critical role in regulating breast cancer progression and therapeutic resistance. An improved understanding of both the features and drivers…”
Get full text

Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer by Carrot-Zhang, Jian, Chambwe, Nyasha, Damrauer, Jeffrey S., Knijnenburg, Theo A., Robertson, A. Gordon, Yau, Christina, Zhou, Wanding, Berger, Ashton C., Huang, Kuan-lin, Newberg, Justin Y., Mashl, R. Jay, Romanel, Alessandro, Sayaman, Rosalyn W., Demichelis, Francesca, Felau, Ina, Frampton, Garrett M., Han, Seunghun, Hoadley, Katherine A., Kemal, Anab, Laird, Peter W., Lazar, Alexander J., Le, Xiuning, Oak, Ninad, Shen, Hui, Wong, Christopher K., Zenklusen, Jean C., Ziv, Elad, Aguet, Francois, Ding, Li, Demchok, John A., Mensah, Michael K.A., Caesar-Johnson, Samantha, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Alfoldi, Jessica, Karczewski, Konrad J., MacArthur, Daniel G., Meyerson, Matthew, Benz, Christopher, Stuart, Joshua M., Cherniack, Andrew D., Beroukhim, Rameen

“…We evaluated ancestry effects on mutation rates, DNA methylation, and mRNA and miRNA expression among 10,678 patients across 33 cancer types from The Cancer…”
Get full text

Genomic Activation of PPARG Reveals a Candidate Therapeutic Axis in Bladder Cancer by Goldstein, Jonathan T, Berger, Ashton C, Shih, Juliann, Duke, Fujiko F, Furst, Laura, Kwiatkowski, David J, Cherniack, Andrew D, Meyerson, Matthew, Strathdee, Craig A

“…The gene encoding the nuclear receptor PPARγ is activated in bladder cancer, either directly by gene amplification or mutation, or indirectly by mutation of…”
Get full text

Tangent normalization for somatic copy-number inference in cancer genome analysis by Gao, Galen F, Oh, Coyin, Saksena, Gordon, Deng, Davy, Westlake, Lindsay C, Hill, Barbara A, Reich, Michael, Schumacher, Steven E, Berger, Ashton C, Carter, Scott L, Cherniack, Andrew D, Meyerson, Matthew, Tabak, Barbara, Beroukhim, Rameen, Getz, Gad

“…Somatic copy-number alterations (SCNAs) play an important role in cancer development. Systematic noise in sequencing and array data present a significant…”
Get full text

Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer by Viswanathan, Srinivas R., Nogueira, Marina F., Buss, Colin G., Krill-Burger, John M., Wawer, Mathias J., Malolepsza, Edyta, Berger, Ashton C., Choi, Peter S., Shih, Juliann, Taylor, Alison M., Tanenbaum, Benjamin, Pedamallu, Chandra Sekhar, Cherniack, Andrew D., Tamayo, Pablo, Strathdee, Craig A., Lage, Kasper, Carr, Steven A., Schenone, Monica, Bhatia, Sangeeta N., Vazquez, Francisca, Tsherniak, Aviad, Hahn, William C., Meyerson, Matthew

“…Functional redundancy shared by paralog genes may afford protection against genetic perturbations, but it can also result in genetic vulnerabilities due to…”
Get full text

Ancestry-specific predisposing germline variants in cancer by Oak, Ninad, Cherniack, Andrew D, Mashl, R Jay, Hirsch, Fred R, Ding, Li, Beroukhim, Rameen, Gümüş, Zeynep H, Plon, Sharon E, Huang, Kuan-Lin

“…Distinct prevalence of inherited genetic predisposition may partially explain the difference of cancer risks across ancestries. Ancestry-specific analyses of…”
Get full text

Analysis of germline-driven ancestry-associated gene expression in cancers by Chambwe, Nyasha, Sayaman, Rosalyn W., Hu, Donglei, Huntsman, Scott, Carrot-Zhang, Jian, Berger, Ashton C., Han, Seunghun, Meyerson, Matthew, Damrauer, Jeffrey S., Hoadley, Katherine A., Felau, Ina, Demchok, John A., Mensah, Michael K.A., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Knijnenburg, Theo A., Robertson, A. Gordon, Yau, Christina, Benz, Christopher, Huang, Kuan-lin, Newberg, Justin Y., Frampton, Garrett M., Mashl, R. Jay, Ding, Li, Romanel, Alessandro, Demichelis, Francesca, Zhou, Wanding, Laird, Peter W., Shen, Hui, Wong, Christopher K., Stuart, Joshua M., Lazar, Alexander J., Le, Xiuning, Oak, Ninad, Kemal, Anab, Caesar-Johnson, Samantha, Zenklusen, Jean C., Ziv, Elad, Beroukhim, Rameen, Cherniack, Andrew D.

“…Differential mRNA expression between ancestry groups can be explained by both genetic and environmental factors. We outline a computational workflow to…”
Get full text

Analytical protocol to identify local ancestry-associated molecular features in cancer by Carrot-Zhang, Jian, Han, Seunghun, Zhou, Wanding, Damrauer, Jeffrey S., Kemal, Anab, Berger, Ashton C., Meyerson, Matthew, Hoadley, Katherine A., Felau, Ina, Caesar-Johnson, Samantha, Demchok, John A., Mensah, Michael K.A., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Chambwe, Nyasha, Knijnenburg, Theo A., Robertson, A. Gordon, Yau, Christina, Benz, Christopher, Huang, Kuan-lin, Newberg, Justin, Frampton, Garret, Mashl, R. Jay, Ding, Li, Romanel, Alessandro, Demichelis, Francesca, Sayaman, Rosalyn W., Ziv, Elad, Laird, Peter W., Shen, Hui, Wong, Christopher K., Stuart, Joshua M., Lazar, Alexander J., Le, Xiuning, Oak, Ninad, Cherniack, Andrew D., Beroukhim, Rameen

“…People of different ancestries vary in cancer risk and outcome, and their molecular differences may indicate sources of these variations. Determining the…”
Get full text

Abstract 1026: Oncogenic alterations in FGFR3 and ERBB2 lead to ligand-independent activation of PPARG in bladder cancer by Goldstein, Jonathan T., Berger, Ashton C., Strathdee, Craig A., Meyerson, Matthew

“…Abstract PPARG is genomically activated in muscle-invasive bladder cancer through focal PPARG gene amplification and hotspot mutations in its heterodimer…”
Get full text

Abstract 3002: Genome engineering approaches to generate models of chromosome arm-level cancer aneuploidy by Taylor, Alison Marie, Zhang, Xiaoyang, Shih, Juliann, Ha, Gavin, Gao, Galen F., Berger, Ashton C., Cherniack, Andrew D., Beroukhim, Rameen, Meyerson, Matthew

“…Abstract Aneuploidy, whole chromosome or chromosome arm copy number imbalance, is a near-universal characteristic of human cancers. Although yeast and…”
Get full text

Abstract 3003: Loss of heterozygosity of essential genes represents a novel class of cancer vulnerabilities by Nichols, Caitlin A., Paolella, Brenton R., Gibson, William J., Brown, Meredith S., Urbanski, Laura M., Kosmicki, Jack A., Busanovich, John P., Berger, Ashton C., Gao, Galen F., Cherniack, Andrew D., Beroukhim, Rameen

“…Abstract Despite progress in precision cancer drug discovery, few highly selective therapies exist in the clinic, creating the need for additional therapeutic…”
Get full text

Abstract 3413: A pan-cancer atlas of genomic, epigenomic and transcriptomic alterations in the TGF-β pathway by Korkut, Anil, Zaidi, Sobia, Kanchi, Rupa, Berger, Ashton C., Robertson, Gordon, Kwong, Lawrence N., Datto, Mike, Roszik, Jason, Ling, Shiyun, Schultz, Andre, Ravikumar, Visweswaran, Manyam, Ganiraju, Rao, Arvind, Shelley, Simon, Liu, Yuexin, Ju, Zhenlin, Hansel, Donna, Velasco, Guillermo de, Pennathur, Arjun, Andersen, Jesper B., O'Rourke, Colm J., Ohshiro, Kazufumi, Jogunoori, Wilma, Gough, Nancy, Li, Shulin, Osmanbeyoglu, Hatice, Houseman, Andres, Rao, Shuyun, Wiznerowicz, Maciej, Chen, Jian, Gu, Shoujun, Ma, Wencai, Zhang, Jiexin, Tong, Pan, Cherniack, Andrew D., Deng, Chuxia, Resar-Smith, Linda, Ajani, Jaffer, Network, The Cancer Genome Atlas Research, Weinstein, John N., Mishra, Lopa, Akbani, Rehan

“…Abstract The TGF-β pathway is a multifunctional signaling cascade with context-dependent roles in diverse biologic processes, including tumor promotion or…”
Get full text