Genetic determinants of cellular addiction to DNA polymerase theta von Feng, Wanjuan, Simpson, Dennis A., Carvajal-Garcia, Juan, Price, Brandon A., Kumar, Rashmi J., Mose, Lisle E., Wood, Richard D., Rashid, Naim, Purvis, Jeremy E., Parker, Joel S., Ramsden, Dale A., Gupta, Gaorav P.

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ABRA: improved coding indel detection via assembly-based realignment von Mose, Lisle E, Wilkerson, Matthew D, Hayes, D Neil, Perou, Charles M, Parker, Joel S

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Prognostic value of B cells in cutaneous melanoma von Selitsky, Sara R, Mose, Lisle E, Smith, Christof C, Chai, Shengjie, Hoadley, Katherine A, Dittmer, Dirk P, Moschos, Stergios J, Parker, Joel S, Vincent, Benjamin G

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Germline Analysis from Tumor-Germline Sequencing Dyads to Identify Clinically Actionable Secondary Findings von Seifert, Bryce A, O'Daniel, Julianne M, Amin, Krunal, Marchuk, Daniel S, Patel, Nirali M, Parker, Joel S, Hoyle, Alan P, Mose, Lisle E, Marron, Andrew, Hayward, Michele C, Bizon, Christopher, Wilhelmsen, Kirk C, Evans, James P, Earp, 3rd, H Shelton, Sharpless, Norman E, Hayes, D Neil, Berg, Jonathan S

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Virus expression detection reveals RNA-sequencing contamination in TCGA von Selitsky, Sara R., Marron, David, Hollern, Daniel, Mose, Lisle E., Hoadley, Katherine A., Jones, Corbin, Parker, Joel S., Dittmer, Dirk P., Perou, Charles M.

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Integrated RNA and DNA sequencing improves mutation detection in low purity tumors von Wilkerson, Matthew D, Cabanski, Christopher R, Sun, Wei, Hoadley, Katherine A, Walter, Vonn, Mose, Lisle E, Troester, Melissa A, Hammerman, Peter S, Parker, Joel S, Perou, Charles M, Hayes, D Neil

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SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling von Silva, Grace O, Siegel, Marni B, Mose, Lisle E, Parker, Joel S, Sun, Wei, Perou, Charles M, Chen, Mengjie

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A P53-Independent DNA Damage Response Suppresses Oncogenic Proliferation and Genome Instability von Fagan-Solis, Katerina D., Simpson, Dennis A., Kumar, Rashmi J., Martelotto, Luciano G., Mose, Lisle E., Rashid, Naim U., Ho, Alice Y., Powell, Simon N., Wen, Y. Hannah, Parker, Joel S., Reis-Filho, Jorge S., Petrini, John H.J., Gupta, Gaorav P.

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Translating transcriptomic findings from cancer model systems to humans through joint dimension reduction von Price, Brandon A., Marron, J. S., Mose, Lisle E., Perou, Charles M., Parker, Joel S.

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Improved indel detection in DNA and RNA via realignment with ABRA2 von Mose, Lisle E, Perou, Charles M, Parker, Joel S

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Genomic characterization of rare molecular subclasses of hepatocellular carcinoma von Damrauer, Jeffrey S., Smith, Markia A., Walter, Vonn, Thennavan, Aatish, Mose, Lisle E., Selitsky, Sara R., Hoadley, Katherine A.

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Epstein-Barr Virus-Positive Cancers Show Altered B-Cell Clonality von Selitsky, Sara R, Marron, David, Mose, Lisle E, Parker, Joel S, Dittmer, Dirk P

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Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer von Mose, Lisle E, Selitsky, Sara R, Bixby, Lisa M, Marron, David L, Iglesia, Michael D, Serody, Jonathan S, Perou, Charles M, Vincent, Benjamin G, Parker, Joel S

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Claudin-low bladder tumors are immune infiltrated and actively immune suppressed von Kardos, Jordan, Chai, Shengjie, Mose, Lisle E, Selitsky, Sara R, Krishnan, Bhavani, Saito, Ryoichi, Iglesia, Michael D, Milowsky, Matthew I, Parker, Joel S, Kim, William Y, Vincent, Benjamin G

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Rad18 mediates specific mutational signatures and shapes the genomic landscape of carcinogen-induced tumors in vivo von Lou, Jitong, Yang, Yang, Gu, Qisheng, Price, Brandon A, Qiu, Yuheng, Fedoriw, Yuri, Desai, Siddhi, Mose, Lisle E, Chen, Brian, Tateishi, Satoshi, Parker, Joel S, Vaziri, Cyrus, Wu, Di

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Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer von Ciriello, Giovanni, Gatza, Michael L., Wilkerson, Matthew D., Rhie, Suhn K., Pastore, Alessandro, McLellan, Michael, Bowlby, Reanne, Lester, Susan C., Tse, Gary M.K., Chen, Yunn-Yi, Jensen, Kristin, Johnson, Nicole B., Mills, Gordon B., Robertson, Gordon, Benz, Christopher, Sander, Chris, Hoadley, Katherine A., King, Tari A., Akbani, Rehan, Auman, J. Todd, Balasundaram, Miruna, Barr, Thomas, Beck, Andrew, Berrios, Mario, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bowlby, Reanne, Brooks, Denise, Cherniack, Andrew D., Chin, Lynda, Davidsen, Tanja, Demchok, John A., Dennison, Jennifer B., Ding, Li, Ferguson, Martin L., Gabriel, Stacey B., Gao, JianJiong, Gastier-Foster, Julie M., Gatza, Michael L., Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Gibson, William J., Hayes, D. Neil, Heiman, David I., Hoadley, Katherine A., Holbrook, Andrea, Hoyle, Alan P., Hu, Hai, Hutter, Carolyn M., Jefferys, Stuart R., Jones, Steven J.M., Ju, Zhenlin, Laird, Peter W., Lawrence, Michael S., Leraas, Kristen M., Lin, Pei, Liu, Jia, Liu, Wenbin, Maglinte, Dennis T., Mardis, Elaine, Marra, Marco A., McAllister, Cynthia, McLellan, Michael, Meng, Shaowu, Mills, Gordon B., Mose, Lisle E., Mungall, Andrew J., Naresh, Rashi, Noble, Michael S., Olopade, Olufunmilayo, Perou, Charles M., Saksena, Gordon, Schumacher, Steven E., Ramirez, Nilsa C., Rathmell, W. Kimryn, Roach, Jeffrey, Sander, Chris, Sheth, Margi, Shi, Yan, Shih, Juliann, Shelley, Carl Simon, Simons, Janae V., Sofia, Heidi J., Sougnez, Carrie, Sun, Charlie, Van Den Berg, David J., Wan, Yunhu, Wang, Zhining, Wise, Lisa, Wiznerowicz, Maciej, Wu, Junyuan, Yang, Liming, Yau, Christina, Zack, Travis I., Zhang, Hailei, Zhang, Jiashan, Perou, Charles M.

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Abstract 1678: Accurate detection of expressed variation in RNA-seq von Mose, Lisle E., Marron, David, Parker, Joel S.

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Integrative Molecular Characterization of Malignant Pleural Mesothelioma von Hmeljak, Julija, Sanchez-Vega, Francisco, Hoadley, Katherine A, Shih, Juliann, Stewart, Chip, Heiman, David, Tarpey, Patrick, Danilova, Ludmila, Drill, Esther, Gibb, Ewan A, Bowlby, Reanne, Kanchi, Rupa, Osmanbeyoglu, Hatice U, Sekido, Yoshitaka, Takeshita, Jumpei, Newton, Yulia, Graim, Kiley, Gupta, Manaswi, Gay, Carl M, Diao, Lixia, Gibbs, David L, Thorsson, Vesteinn, Iype, Lisa, Kantheti, Havish, Severson, David T, Ravegnini, Gloria, Desmeules, Patrice, Jungbluth, Achim A, Travis, William D, Dacic, Sanja, Chirieac, Lucian R, Galateau-Sallé, Françoise, Fujimoto, Junya, Husain, Aliya N, Silveira, Henrique C, Rusch, Valerie W, Rintoul, Robert C, Pass, Harvey, Kindler, Hedy, Zauderer, Marjorie G, Kwiatkowski, David J, Bueno, Raphael, Tsao, Anne S, Creaney, Jenette, Lichtenberg, Tara, Leraas, Kristen, Bowen, Jay, Felau, Ina, Zenklusen, Jean Claude, Akbani, Rehan, Cherniack, Andrew D, Byers, Lauren A, Noble, Michael S, Fletcher, Jonathan A, Robertson, A Gordon, Shen, Ronglai, Aburatani, Hiroyuki, Robinson, Bruce W, Campbell, Peter, Ladanyi, Marc

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Integrated Molecular Characterization of Uterine Carcinosarcoma von Cherniack, Andrew D., Murray, Bradley A., Hu, Xin, Ling, Shiyun, Soslow, Robert A., Zuna, Rosemary E., Laird, Peter W., Kucherlapati, Raju, Mills, Gordon B., Akbani, Rehan, Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Baylin, Stephen B., Bodenheimer, Tom, Bogomolniy, Faina, Brooks, Denise, Carlsen, Rebecca, Cherniack, Andrew D., Cho, Juok, Chuah, Eric, Chudamani, Sudha, David, Mutch, Ferguson, Martin L., Frick, Jessica, Gabriel, Stacey, Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Gupta, Manaswi, Heiman, David I., Hess, Julian, Hoffmann, Robert, Holt, Robert A., Hu, Xin, Hutter, Carolyn M., Jefferys, Stuart R., Kanchi, Rupa S., Kandoth, Cyriac, Kerr, Sarah, Kim, Jaegil, Lai, Phillip H., Laird, Peter W., Lander, Eric, Lawrence, Michael S., Lee, Darlene, Leshchiner, Ignaty, Levine, Douglas A., Lichtenberg, Tara M., Ling, Shiyun, Liu, Jia, Liu, Wenbin, Lolla, Laxmi, Lu, Yiling, Ma, Yussanne, Maglinte, Dennis T., Marra, Marco A., Mayo, Michael, Meng, Shaowu, Meyerson, Matthew, Moore, Richard A., Mose, Lisle E., Mungall, Karen, Murray, Bradley A., Naresh, Rashi, Parker, Joel S., Perou, Charles M., Radenbaugh, Amie J., Ramirez, Nilsa C., Rathmell, W. Kimryn, Roach, Jeffrey, Robertson, A. Gordon, Sadeghi, Sara, Saksena, Gordon, Salvesen, Helga B., Sheth, Margi, Shi, Yan, Shih, Juliann, Skelly, Tara, Sofia, Heidi J., Soloway, Matthew G., Sun, Charlie, Tan, Donghui, Tarnuzzer, Roy, Thorne, Leigh B., Tseng, Jill, Veluvolu, Umadevi, Verhaak, Roel G.W., Voet, Doug, Wan, Yunhu, Wang, Chen, Weisenberger, Daniel J., Wilkerson, Matthew D., Winterhoff, Boris, Wong, Tina, Yang, Liming, Zhang, Hailei, Zhu, Jing-chun, Zuna, Rosemary E., Weinstein, John N.

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Abstract 3592: Improved indel detection in RNA-seq data via assembly based re-alignment reveals expressed Epidermal Growth Factor Receptor indels in Lung Adenocarcinoma von Mose, Lisle E., Hayes, D. Neil, Perou, Charles M., Parker, Joel S.

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