Passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features von Buisson, Rémi, Langenbucher, Adam, Bowen, Danae, Kwan, Eugene E, Benes, Cyril H, Zou, Lee, Lawrence, Michael S

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Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples von Cibulskis, Kristian, Lawrence, Michael S, Carter, Scott L, Sivachenko, Andrey, Jaffe, David, Sougnez, Carrie, Gabriel, Stacey, Meyerson, Matthew, Lander, Eric S, Getz, Gad

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Cell-of-origin chromatin organization shapes the mutational landscape of cancer von Polak, Paz, Karlić, Rosa, Koren, Amnon, Thurman, Robert, Sandstrom, Richard, Lawrence, Michael S., Reynolds, Alex, Rynes, Eric, Vlahoviček, Kristian, Stamatoyannopoulos, John A., Sunyaev, Shamil R.

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Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair von Haradhvala, Nicholas J., Polak, Paz, Stojanov, Petar, Covington, Kyle R., Shinbrot, Eve, Hess, Julian M., Rheinbay, Esther, Kim, Jaegil, Maruvka, Yosef E., Braunstein, Lior Z., Kamburov, Atanas, Hanawalt, Philip C., Wheeler, David A., Koren, Amnon, Lawrence, Michael S., Getz, Gad

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Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients von van de Wetering, Marc, Francies, Hayley E., Francis, Joshua M., Bounova, Gergana, Iorio, Francesco, Pronk, Apollo, van Houdt, Winan, van Gorp, Joost, Taylor-Weiner, Amaro, Kester, Lennart, McLaren-Douglas, Anne, Blokker, Joyce, Jaksani, Sridevi, Bartfeld, Sina, Volckman, Richard, van Sluis, Peter, Li, Vivian S.W., Seepo, Sara, Sekhar Pedamallu, Chandra, Cibulskis, Kristian, Carter, Scott L., McKenna, Aaron, Lawrence, Michael S., Lichtenstein, Lee, Stewart, Chip, Koster, Jan, Versteeg, Rogier, van Oudenaarden, Alexander, Saez-Rodriguez, Julio, Vries, Robert G.J., Getz, Gad, Wessels, Lodewyk, Stratton, Michael R., McDermott, Ultan, Meyerson, Matthew, Garnett, Mathew J., Clevers, Hans

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Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes von Shukla, Sachet A, Rooney, Michael S, Rajasagi, Mohini, Tiao, Grace, Dixon, Philip M, Lawrence, Michael S, Stevens, Jonathan, Lane, William J, Dellagatta, Jamie L, Steelman, Scott, Sougnez, Carrie, Cibulskis, Kristian, Kiezun, Adam, Hacohen, Nir, Brusic, Vladimir, Wu, Catherine J, Getz, Gad

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Stromal Microenvironment Shapes the Intratumoral Architecture of Pancreatic Cancer von Ligorio, Matteo, Sil, Srinjoy, Malagon-Lopez, Jose, Nieman, Linda T., Misale, Sandra, Di Pilato, Mauro, Ebright, Richard Y., Karabacak, Murat N., Kulkarni, Anupriya S., Liu, Ann, Vincent Jordan, Nicole, Franses, Joseph W., Philipp, Julia, Kreuzer, Johannes, Desai, Niyati, Arora, Kshitij S., Rajurkar, Mihir, Horwitz, Elad, Neyaz, Azfar, Tai, Eric, Magnus, Neelima K.C., Vo, Kevin D., Yashaswini, Chittampalli N., Marangoni, Francesco, Boukhali, Myriam, Fatherree, Jackson P., Damon, Leah J., Xega, Kristina, Desai, Rushil, Choz, Melissa, Bersani, Francesca, Langenbucher, Adam, Thapar, Vishal, Morris, Robert, Wellner, Ulrich F., Schilling, Oliver, Lawrence, Michael S., Liss, Andrew S., Rivera, Miguel N., Deshpande, Vikram, Benes, Cyril H., Maheswaran, Shyamala, Haber, Daniel A., Fernandez-Del-Castillo, Carlos, Ferrone, Cristina R., Haas, Wilhelm, Aryee, Martin J., Ting, David T.

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APOBEC3A and APOBEC3B Activities Render Cancer Cells Susceptible to ATR Inhibition von Buisson, Rémi, Lawrence, Michael S, Benes, Cyril H, Zou, Lee

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Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes von Leiserson, Mark D M, Vandin, Fabio, Wu, Hsin-Ta, Dobson, Jason R, Eldridge, Jonathan V, Thomas, Jacob L, Papoutsaki, Alexandra, Kim, Younhun, Niu, Beifang, McLellan, Michael, Lawrence, Michael S, Gonzalez-Perez, Abel, Tamborero, David, Cheng, Yuwei, Ryslik, Gregory A, Lopez-Bigas, Nuria, Getz, Gad, Ding, Li, Raphael, Benjamin J

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Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing von Helman, Elena, Lawrence, Michael S, Stewart, Chip, Sougnez, Carrie, Getz, Gad, Meyerson, Matthew

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Widespread Genetic Heterogeneity in Multiple Myeloma: Implications for Targeted Therapy von Lohr, Jens G., Stojanov, Petar, Carter, Scott L., Cruz-Gordillo, Peter, Lawrence, Michael S., Auclair, Daniel, Sougnez, Carrie, Knoechel, Birgit, Gould, Joshua, Saksena, Gordon, Cibulskis, Kristian, McKenna, Aaron, Chapman, Michael A., Straussman, Ravid, Levy, Joan, Perkins, Louise M., Keats, Jonathan J., Schumacher, Steven E., Rosenberg, Mara, Anderson, Kenneth C., Richardson, Paul, Krishnan, Amrita, Lonial, Sagar, Kaufman, Jonathan, Siegel, David S., Vesole, David H., Roy, Vivek, Rivera, Candido E., Rajkumar, S. Vincent, Kumar, Shaji, Fonseca, Rafael, Ahmann, Greg J., Bergsagel, P. Leif, Stewart, A. Keith, Hofmeister, Craig C., Efebera, Yvonne A., Jagannath, Sundar, Chari, Ajai, Trudel, Suzanne, Reece, Donna, Wolf, Jeffrey, Martin, Thomas, Zimmerman, Todd, Rosenbaum, Cara, Jakubowiak, Andrzej J., Lebovic, Daniel, Vij, Ravi, Stockerl-Goldstein, Keith, Getz, Gad, Golub, Todd R.

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An extended APOBEC3A mutation signature in cancer von Langenbucher, Adam, Bowen, Danae, Sakhtemani, Ramin, Bournique, Elodie, Wise, Jillian F., Zou, Lee, Bhagwat, Ashok S., Buisson, Rémi, Lawrence, Michael S.

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Pan-cancer patterns of somatic copy number alteration von 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

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Punctuated Evolution of Prostate Cancer Genomes von Baca, Sylvan C., Prandi, Davide, Lawrence, Michael S., Mosquera, Juan Miguel, Romanel, Alessandro, Drier, Yotam, Park, Kyung, Kitabayashi, Naoki, MacDonald, Theresa Y., Ghandi, Mahmoud, Van Allen, Eliezer, Kryukov, Gregory V., Sboner, Andrea, Theurillat, Jean-Philippe, Soong, T. David, Nickerson, Elizabeth, Auclair, Daniel, Tewari, Ashutosh, Beltran, Himisha, Onofrio, Robert C., Boysen, Gunther, Guiducci, Candace, Barbieri, Christopher E., Cibulskis, Kristian, Sivachenko, Andrey, Carter, Scott L., Saksena, Gordon, Voet, Douglas, Ramos, Alex H., Winckler, Wendy, Cipicchio, Michelle, Ardlie, Kristin, Kantoff, Philip W., Berger, Michael F., Gabriel, Stacey B., Golub, Todd R., Meyerson, Matthew, Lander, Eric S., Elemento, Olivier, Getz, Gad, Demichelis, Francesca, Rubin, Mark A., Garraway, Levi A.

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Quantification of ongoing APOBEC3A activity in tumor cells by monitoring RNA editing at hotspots von Jalili, Pégah, Bowen, Danae, Langenbucher, Adam, Park, Shinho, Aguirre, Kevin, Corcoran, Ryan B., Fleischman, Angela G., Lawrence, Michael S., Zou, Lee, Buisson, Rémi

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Comprehensive assessment of cancer missense mutation clustering in protein structures von Kamburov, Atanas, Lawrence, Michael S., Polak, Paz, Leshchiner, Ignaty, Lage, Kasper, Golub, Todd R., Lander, Eric S., Getz, Gad

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MET Alterations Are a Recurring and Actionable Resistance Mechanism in ALK-Positive Lung Cancer von Dagogo-Jack, Ibiayi, Yoda, Satoshi, Lennerz, Jochen K., Langenbucher, Adam, Lin, Jessica J., Rooney, Marguerite M., Prutisto-Chang, Kylie, Oh, Audris, Adams, Nathaniel A., Yeap, Beow Y., Chin, Emily, Do, Andrew, Marble, Hetal D., Stevens, Sara E., Digumarthy, Subba R., Saxena, Ashish, Nagy, Rebecca J., Benes, Cyril H., Azzoli, Christopher G., Lawrence, Michael S., Gainor, Justin F., Shaw, Alice T., Hata, Aaron N.

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A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer von Polak, Paz, Kim, Jaegil, Braunstein, Lior Z, Karlic, Rosa, Haradhavala, Nicholas J, Tiao, Grace, Rosebrock, Daniel, Livitz, Dimitri, Kübler, Kirsten, Mouw, Kent W, Kamburov, Atanas, Maruvka, Yosef E, Leshchiner, Ignaty, Lander, Eric S, Golub, Todd R, Zick, Aviad, Orthwein, Alexandre, Lawrence, Michael S, Batra, Rajbir N, Caldas, Carlos, Haber, Daniel A, Laird, Peter W, Shen, Hui, Ellisen, Leif W, D'Andrea, Alan D, Chanock, Stephen J, Foulkes, William D, Getz, Gad

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Integrative and comparative genomic analysis of HPV-positive and HPV-negative head and neck squamous cell carcinomas von Seiwert, Tanguy Y, Zuo, Zhixiang, Keck, Michaela K, Khattri, Arun, Pedamallu, Chandra S, Stricker, Thomas, Brown, Christopher, Pugh, Trevor J, Stojanov, Petar, Cho, Juok, Lawrence, Michael S, Getz, Gad, Brägelmann, Johannes, DeBoer, Rebecca, Weichselbaum, Ralph R, Langerman, Alexander, Portugal, Louis, Blair, Elizabeth, Stenson, Kerstin, Lingen, Mark W, Cohen, Ezra E W, Vokes, Everett E, White, Kevin P, Hammerman, Peter S

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The Mutational Landscape of Head and Neck Squamous Cell Carcinoma von Stransky, Nicolas, Egloff, Ann Marie, Tward, Aaron D., Kostic, Aleksandar D., Cibulskis, Kristian, Sivachenko, Andrey, Kryukov, Gregory V., Lawrence, Michael S., Sougnez, Carrie, McKenna, Aaron, Shefler, Erica, Ramos, Alex H., Stojanov, Petar, Carter, Scott L., Voet, Douglas, Cortés, Maria L., Auclair, Daniel, Berger, Michael F., Saksena, Gordon, Guiducci, Candace, Onofrio, Robert C., Parkin, Melissa, Romkes, Marjorie, Weissfeld, Joel L., Seethala, Raja R., Wang, Lin, Rangel-Escareño, Claudia, Fernandez-Lopez, Juan Carlos, Hidalgo-Miranda, Alfredo, Melendez-Zajgla, Jorge, Winckler, Wendy, Ardlie, Kristin, Gabriel, Stacey B., Meyerson, Matthew, Lander, Eric S., Getz, Gad, Golub, Todd R., Garraway, Levi A., Grandis, Jennifer R.

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