Search Results - "Beroukhim, Rameen"

Genomic evolution of cancer models: perils and opportunities by Ben-David, Uri, Beroukhim, Rameen, Golub, Todd R.

“…Cancer research relies on model systems, which reflect the biology of actual human tumours to only a certain extent. One important feature of human cancer is…”
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Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate by Chakraborty, Abhishek A, Laukka, Tuomas, Myllykoski, Matti, Ringel, Alison E, Booker, Matthew A, Tolstorukov, Michael Y, Meng, Yuzhong Jeff, Meier, Samuel R, Jennings, Rebecca B, Creech, Amanda L, Herbert, Zachary T, McBrayer, Samuel K, Olenchock, Benjamin A, Jaffe, Jacob D, Haigis, Marcia C, Beroukhim, Rameen, Signoretti, Sabina, Koivunen, Peppi, Kaelin, Jr, William G

“…Oxygen sensing is central to metazoan biology and has implications for human disease. Mammalian cells express multiple oxygen-dependent enzymes called…”
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Genetic and transcriptional evolution alters cancer cell line drug response by Ben-David, Uri, Siranosian, Benjamin, Ha, Gavin, Tang, Helen, Oren, Yaara, Hinohara, Kunihiko, Strathdee, Craig A., Dempster, Joshua, Lyons, Nicholas J., Burns, Robert, Nag, Anwesha, Kugener, Guillaume, Cimini, Beth, Tsvetkov, Peter, Maruvka, Yosef E., O’Rourke, Ryan, Garrity, Anthony, Tubelli, Andrew A., Bandopadhayay, Pratiti, Tsherniak, Aviad, Vazquez, Francisca, Wong, Bang, Birger, Chet, Ghandi, Mahmoud, Thorner, Aaron R., Bittker, Joshua A., Meyerson, Matthew, Getz, Gad, Beroukhim, Rameen, Golub, Todd R.

“…Human cancer cell lines are the workhorse of cancer research. Although cell lines are known to evolve in culture, the extent of the resultant genetic and…”
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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…”
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GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers by Mermel, Craig H, Schumacher, Steven E, Hill, Barbara, Meyerson, Matthew L, Beroukhim, Rameen, Getz, Gad

“…We describe methods with enhanced power and specificity to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By…”
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Cas9 activates the p53 pathway and selects for p53-inactivating mutations by Enache, Oana M., Rendo, Veronica, Abdusamad, Mai, Lam, Daniel, Davison, Desiree, Pal, Sangita, Currimjee, Naomi, Hess, Julian, Pantel, Sasha, Nag, Anwesha, Thorner, Aaron R., Doench, John G., Vazquez, Francisca, Beroukhim, Rameen, Golub, Todd R., Ben-David, Uri

“…Cas9 is commonly introduced into cell lines to enable CRISPR–Cas9-mediated genome editing. Here, we studied the genetic and transcriptional consequences of…”
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SvABA: genome-wide detection of structural variants and indels by local assembly by Wala, Jeremiah A, Bandopadhayay, Pratiti, Greenwald, Noah F, O'Rourke, Ryan, Sharpe, Ted, Stewart, Chip, Schumacher, Steve, Li, Yilong, Weischenfeldt, Joachim, Yao, Xiaotong, Nusbaum, Chad, Campbell, Peter, Getz, Gad, Meyerson, Matthew, Zhang, Cheng-Zhong, Imielinski, Marcin, Beroukhim, Rameen

“…Structural variants (SVs), including small insertion and deletion variants (indels), are challenging to detect through standard alignment-based variant calling…”
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Landscape of Genomic Alterations in Pituitary Adenomas by Bi, Wenya Linda, Horowitz, Peleg, Greenwald, Noah F, Abedalthagafi, Malak, Agarwalla, Pankaj K, Gibson, Wiliam J, Mei, Yu, Schumacher, Steven E, Ben-David, Uri, Chevalier, Aaron, Carter, Scott, Tiao, Grace, Brastianos, Priscilla K, Ligon, Azra H, Ducar, Matthew, MacConaill, Laura, Laws, Jr, Edward R, Santagata, Sandro, Beroukhim, Rameen, Dunn, Ian F

“…Pituitary adenomas are the second most common primary brain tumor, yet their genetic profiles are incompletely understood. We performed whole-exome sequencing…”
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Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing by Viswanathan, Srinivas R., Ha, Gavin, Hoff, Andreas M., Wala, Jeremiah A., Carrot-Zhang, Jian, Whelan, Christopher W., Haradhvala, Nicholas J., Freeman, Samuel S., Reed, Sarah C., Rhoades, Justin, Polak, Paz, Cipicchio, Michelle, Wankowicz, Stephanie A., Wong, Alicia, Kamath, Tushar, Zhang, Zhenwei, Gydush, Gregory J., Rotem, Denisse, Love, J. Christopher, Getz, Gad, Gabriel, Stacey, Zhang, Cheng-Zhong, Dehm, Scott M., Nelson, Peter S., Van Allen, Eliezer M., Choudhury, Atish D., Adalsteinsson, Viktor A., Beroukhim, Rameen, Taplin, Mary-Ellen, Meyerson, Matthew

“…Nearly all prostate cancer deaths are from metastatic castration-resistant prostate cancer (mCRPC), but there have been few whole-genome sequencing (WGS)…”
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Absolute quantification of somatic DNA alterations in human cancer by Carter, Scott L, Cibulskis, Kristian, Helman, Elena, McKenna, Aaron, Shen, Hui, Zack, Travis, Laird, Peter W, Onofrio, Robert C, Winckler, Wendy, Weir, Barbara A, Beroukhim, Rameen, Pellman, David, Levine, Douglas A, Lander, Eric S, Meyerson, Matthew, Getz, Gad

“…Tumors vary in their ratio of normal to cancerous cells and in their genomic copy number. Carter et al . describe an analytic method for inferring the purity…”
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Pan-cancer patterns of somatic copy number alteration by Zack, Travis I, Schumacher, Steven E, Carter, Scott L, Cherniack, Andrew D, Saksena, Gordon, Tabak, Barbara, Lawrence, Michael S, Zhang, Cheng-Zhong, Wala, Jeremiah, Mermel, Craig H, Sougnez, Carrie, Gabriel, Stacey B, Hernandez, Bryan, Shen, Hui, Laird, Peter W, Getz, Gad, Meyerson, Matthew, Beroukhim, Rameen

“…Rameen Beroukhim and colleagues analyzed somatic structural alterations in 12 tumor types. Whole-genome doubling was found in over a third of all cancers,…”
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Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition by Wong, Gabrielle S., Zhou, Jin, Liu, Jie Bin, Wu, Zhong, Xu, Xinsen, Li, Tianxia, Xu, David, Schumacher, Steven E., Puschhof, Jens, McFarland, James, Zou, Charles, Dulak, Austin, Henderson, Les, Xu, Peng, O’Day, Emily, Rendak, Rachel, Liao, Wei-li, Cecchi, Fabiola, Hembrough, Todd, Schwartz, Sarit, Szeto, Christopher, Rustgi, Anil K., Wong, Kwok-Kin, Diehl, J. Alan, Jensen, Karin, Graziano, Francesco, Ruzzo, Annamaria, Fereshetian, Shaunt, Mertins, Philipp, Carr, Steven A., Beroukhim, Rameen, Nakamura, Kenichi, Oki, Eiji, Watanabe, Masayuki, Baba, Hideo, Imamura, Yu, Catenacci, Daniel, Bass, Adam J.

“…The role of KRAS, when activated through canonical mutations, has been well established in cancer 1 . Here we explore a secondary means of KRAS activation in…”
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Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations by Brastianos, Priscilla K, Horowitz, Peleg M, Santagata, Sandro, Jones, Robert T, McKenna, Aaron, Getz, Gad, Ligon, Keith L, Palescandolo, Emanuele, Van Hummelen, Paul, Ducar, Matthew D, Raza, Alina, Sunkavalli, Ashwini, MacConaill, Laura E, Stemmer-Rachamimov, Anat O, Louis, David N, Hahn, William C, Dunn, Ian F, Beroukhim, Rameen

“…Rameen Beroukhim, Ian Dunn, William Hahn and colleagues report genome and exome sequencing of meningiomas. They identified recurrent somatic mutations in AKT1…”
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A molecularly integrated grade for meningioma by Driver, Joseph, Hoffman, Samantha E, Tavakol, Sherwin, Woodward, Eleanor, Maury, Eduardo A, Bhave, Varun, Greenwald, Noah F, Nassiri, Farshad, Aldape, Kenneth, Zadeh, Gelareh, Choudhury, Abrar, Vasudevan, Harish N, Magill, Stephen T, Raleigh, David R, Abedalthagafi, Malak, Aizer, Ayal A, Alexander, Brian M, Ligon, Keith L, Reardon, David A, Wen, Patrick Y, Al-Mefty, Ossama, Ligon, Azra H, Dubuc, Adrian M, Beroukhim, Rameen, Claus, Elizabeth B, Dunn, Ian F, Santagata, Sandro, Linda Bi, Wenya

“…Abstract Background Meningiomas are the most common primary intracranial tumor in adults. Clinical care is currently guided by the World Health Organization…”
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Epigenetic targeting of Hedgehog pathway transcriptional output through BET bromodomain inhibition by Tang, Yujie, Gholamin, Sharareh, Schubert, Simone, Willardson, Minde I, Lee, Alex, Bandopadhayay, Pratiti, Bergthold, Guillame, Masoud, Sabran, Nguyen, Brian, Vue, Nujsaubnusi, Balansay, Brianna, Yu, Furong, Oh, Sekyung, Woo, Pamelyn, Chen, Spenser, Ponnuswami, Anitha, Monje, Michelle, Atwood, Scott X, Whitson, Ramon J, Mitra, Siddhartha, Cheshier, Samuel H, Qi, Jun, Beroukhim, Rameen, Tang, Jean Y, Wechsler-Reya, Rob, Oro, Anthony E, Link, Brian A, Bradner, James E, Cho, Yoon-Jae

“…Cancers dependent on hedgehog pathway signaling are susceptible to the BET bromodomain inhibitor JQ1. Hedgehog signaling drives oncogenesis in several cancers,…”
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The genomic landscape and evolution of endometrial carcinoma progression and abdominopelvic metastasis by Gibson, William J, Hoivik, Erling A, Halle, Mari K, Taylor-Weiner, Amaro, Cherniack, Andrew D, Berg, Anna, Holst, Frederik, Zack, Travis I, Werner, Henrica M J, Staby, Kjersti M, Rosenberg, Mara, Stefansson, Ingunn M, Kusonmano, Kanthida, Chevalier, Aaron, Mauland, Karen K, Trovik, Jone, Krakstad, Camilla, Giannakis, Marios, Hodis, Eran, Woie, Kathrine, Bjorge, Line, Vintermyr, Olav K, Wala, Jeremiah A, Lawrence, Michael S, Getz, Gad, Carter, Scott L, Beroukhim, Rameen, Salvesen, Helga B

“…Helga Salvesen, Rameen Beroukhim, Scott Carter and colleagues study the evolutionary landscape of endometrial cancer by performing whole-exome sequencing of…”
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An in-tumor genetic screen reveals that the BET bromodomain protein, BRD4, is a potential therapeutic target in ovarian carcinoma by Baratta, Maria Giuseppina, Schinzel, Anna C., Zwang, Yaara, Bandopadhayay, Pratiti, Bowman-Colin, Christian, Kutt, Jennifer, Curtis, Jennifer, Piao, Huiying, Wong, Laura C., Kung, Andrew L., Beroukhim, Rameen, Bradner, James E., Drapkin, Ronny, Hahn, William C., Liu, Joyce F., Livingston, David M.

“…High-grade serous ovarian carcinoma (HGSOC) is the most common and aggressive form of epithelial ovarian cancer, for which few targeted therapies exist. To…”
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Genomic landscape of intracranial meningiomas by Bi, Wenya Linda, Abedalthagafi, Malak, Horowitz, Peleg, Agarwalla, Pankaj K, Mei, Yu, Aizer, Ayal A, Brewster, Ryan, Dunn, Gavin P, Al-Mefty, Ossama, Alexander, Brian M, Santagata, Sandro, Beroukhim, Rameen, Dunn, Ian F

“…Meningiomas are the most common primary intracranial neoplasms in adults. Current histopathological grading schemes do not consistently predict their natural…”
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The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset by Ceol, Craig J., Houvras, Yariv, Jane-Valbuena, Judit, Bilodeau, Steve, Orlando, David A., Battisti, Valentine, Fritsch, Lauriane, Lin, William M., Hollmann, Travis J., Ferré, Fabrizio, Bourque, Caitlin, Burke, Christopher J., Turner, Laura, Uong, Audrey, Johnson, Laura A., Beroukhim, Rameen, Mermel, Craig H., Loda, Massimo, Ait-Si-Ali, Slimane, Garraway, Levi A., Young, Richard A., Zon, Leonard I.

“…Oncogenes BRAF(V600E) and SETDB1 in melanoma Transgenic zebrafish carrying the human oncogene BRAF(V600E) , the most common mutation in melanoma patients,…”
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The RasGAP Gene, RASAL2, Is a Tumor and Metastasis Suppressor by McLaughlin, Sara Koenig, Olsen, Sarah Naomi, Dake, Benjamin, De Raedt, Thomas, Lim, Elgene, Bronson, Roderick Terry, Beroukhim, Rameen, Polyak, Kornelia, Brown, Myles, Kuperwasser, Charlotte, Cichowski, Karen

“…RAS genes are commonly mutated in cancer; however, RAS mutations are rare in breast cancer, despite frequent hyperactivation of Ras and ERK. Here, we report…”
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