Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma von 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.

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Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma von Miao, Diana, Margolis, Claire A, Gao, Wenhua, Voss, Martin H, Li, Wei, Martini, Dylan J, Norton, Craig, Bossé, Dominick, Wankowicz, Stephanie M, Cullen, Dana, Horak, Christine, Wind-Rotolo, Megan, Tracy, Adam, Giannakis, Marios, Hodi, Frank Stephen, Drake, Charles G, Ball, Mark W, Allaf, Mohamad E, Snyder, Alexandra, Hellmann, Matthew D, Ho, Thai, Motzer, Robert J, Signoretti, Sabina, Kaelin, Jr, William G, Choueiri, Toni K, Van Allen, Eliezer M

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Response and Acquired Resistance to Everolimus in Anaplastic Thyroid Cancer von Wagle, Nikhil, Grabiner, Brian C, Van Allen, Eliezer M, Amin-Mansour, Ali, Taylor-Weiner, Amaro, Rosenberg, Mara, Gray, Nathanael, Barletta, Justine A, Guo, Yanan, Swanson, Scott J, Ruan, Daniel T, Hanna, Glenn J, Haddad, Robert I, Getz, Gad, Kwiatkowski, David J, Carter, Scott L, Sabatini, David M, Jänne, Pasi A, Garraway, Levi A, Lorch, Jochen H

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Artificial intelligence-aided clinical annotation of a large multi-cancer genomic dataset von Kehl, Kenneth L., Xu, Wenxin, Gusev, Alexander, Bakouny, Ziad, Choueiri, Toni K., Riaz, Irbaz Bin, Elmarakeby, Haitham, Van Allen, Eliezer M., Schrag, Deborah

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Genomic correlates of response to immune checkpoint blockade von Keenan, Tanya E., Burke, Kelly P., Van Allen, Eliezer M.

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Biologically informed deep neural network for prostate cancer discovery von Elmarakeby, Haitham A., Hwang, Justin, Arafeh, Rand, Crowdis, Jett, Gang, Sydney, Liu, David, AlDubayan, Saud H., Salari, Keyan, Kregel, Steven, Richter, Camden, Arnoff, Taylor E., Park, Jihye, Hahn, William C., Van Allen, Eliezer M.

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Dissecting the immunogenomic biology of cancer for biomarker development von Van Allen, Eliezer M., Choueiri, Toni K.

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A model combining clinical and genomic factors to predict response to PD-1/PD-L1 blockade in advanced urothelial carcinoma von Nassar, Amin H., Mouw, Kent W., Jegede, Opeyemi, Shinagare, Atul B., Kim, Jaegil, Liu, Chia-Jen, Pomerantz, Mark, Harshman, Lauren C., Van Allen, Eliezer M., Wei, Xiao X., McGregor, Bradley, Choudhury, Atish D., Preston, Mark A., Dong, Fei, Signoretti, Sabina, Lindeman, Neal I., Bellmunt, Joaquim, Choueiri, Toni K., Sonpavde, Guru, Kwiatkowski, David J.

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Molecular correlates of response to eribulin and pembrolizumab in hormone receptor-positive metastatic breast cancer von Keenan, Tanya E., Guerriero, Jennifer L., Barroso-Sousa, Romualdo, Li, Tianyu, O’Meara, Tess, Giobbie-Hurder, Anita, Tayob, Nabihah, Hu, Jiani, Severgnini, Mariano, Agudo, Judith, Vaz-Luis, Ines, Anderson, Leilani, Attaya, Victoria, Park, Jihye, Conway, Jake, He, Meng Xiao, Reardon, Brendan, Shannon, Erin, Wulf, Gerburg, Spring, Laura M., Jeselsohn, Rinath, Krop, Ian, Lin, Nancy U., Partridge, Ann, Winer, Eric P., Mittendorf, Elizabeth A., Liu, David, Van Allen, Eliezer M., Tolaney, Sara M.

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Intron retention is a source of neoepitopes in cancer von Smart, Alicia C, Margolis, Claire A, Pimentel, Harold, He, Meng Xiao, Miao, Diana, Adeegbe, Dennis, Fugmann, Tim, Wong, Kwok-Kin, Van Allen, Eliezer M

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Identification of cancer driver genes based on nucleotide context von Dietlein, Felix, Weghorn, Donate, Taylor-Weiner, Amaro, Richters, André, Reardon, Brendan, Liu, David, Lander, Eric S., Van Allen, Eliezer M., Sunyaev, Shamil R.

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Beyond conventional immune-checkpoint inhibition — novel immunotherapies for renal cell carcinoma von Braun, David A., Bakouny, Ziad, Hirsch, Laure, Flippot, Ronan, Van Allen, Eliezer M., Wu, Catherine J., Choueiri, Toni K.

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Genomic correlates of response to CTLA-4 blockade in metastatic melanoma von Van Allen, Eliezer M., Miao, Diana, Schilling, Bastian, Shukla, Sachet A., Blank, Christian, Zimmer, Lisa, Sucker, Antje, Hillen, Uwe, Foppen, Marnix H. Geukes, Goldinger, Simone M., Utikal, Jochen, Hassel, Jessica C., Weide, Benjamin, Kaehler, Katharina C., Loquai, Carmen, Mohr, Peter, Gutzmer, Ralf, Dummer, Reinhard, Gabriel, Stacey, Wu, Catherine J., Schadendorf, Dirk, Garraway, Levi A.

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Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer von Beltran, Himisha, Prandi, Davide, Mosquera, Juan Miguel, Benelli, Matteo, Puca, Loredana, Cyrta, Joanna, Marotz, Clarisse, Giannopoulou, Eugenia, Chakravarthi, Balabhadrapatruni V S K, Varambally, Sooryanarayana, Tomlins, Scott A, Nanus, David M, Tagawa, Scott T, Van Allen, Eliezer M, Elemento, Olivier, Sboner, Andrea, Garraway, Levi A, Rubin, Mark A, Demichelis, Francesca

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Genomic Approaches to Understanding Response and Resistance to Immunotherapy von Braun, David A, Burke, Kelly P, Van Allen, Eliezer M

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Compound Genomic Alterations of TP53, PTEN, and RB1 Tumor Suppressors in Localized and Metastatic Prostate Cancer von Hamid, Anis A., Gray, Kathryn P., Shaw, Grace, MacConaill, Laura E., Evan, Carolyn, Bernard, Brandon, Loda, Massimo, Corcoran, Niall M., Van Allen, Eliezer M., Choudhury, Atish D., Sweeney, Christopher J.

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Scaling computational genomics to millions of individuals with GPUs von Taylor-Weiner, Amaro, Aguet, François, Haradhvala, Nicholas J, Gosai, Sager, Anand, Shankara, Kim, Jaegil, Ardlie, Kristin, Van Allen, Eliezer M, Getz, Gad

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Tumor Mutational Burden and PTEN Alterations as Molecular Correlates of Response to PD-1/L1 Blockade in Metastatic Triple-Negative Breast Cancer von Barroso-Sousa, Romualdo, Keenan, Tanya E., Pernas, Sonia, Exman, Pedro, Jain, Esha, Garrido-Castro, Ana C., Hughes, Melissa, Bychkovsky, Brittany, Umeton, Renato, Files, Janet L., Lindeman, Neal I., MacConaill, Laura E., Hodi, F. Stephen, Krop, Ian E., Dillon, Deborah, Winer, Eric P., Wagle, Nikhil, Lin, Nancy U., Mittendorf, Elizabeth A., Van Allen, Eliezer M., Tolaney, Sara M.

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Genomic Evolution after Chemoradiotherapy in Anal Squamous Cell Carcinoma von Mouw, Kent W, Cleary, James M, Reardon, Brendan, Pike, Jonathan, Braunstein, Lior Z, Kim, Jaegil, Amin-Mansour, Ali, Miao, Diana, Damish, Alexis, Chin, Joanna, Ott, Patrick A, Fuchs, Charles S, Martin, Neil E, Getz, Gad, Carter, Scott, Mamon, Harvey J, Hornick, Jason L, Van Allen, Eliezer M, D'Andrea, Alan D

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FiTAc-seq: fixed-tissue ChIP-seq for H3K27ac profiling and super-enhancer analysis of FFPE tissues von Font-Tello, Alba, Kesten, Nikolas, Xie, Yingtian, Taing, Len, Varešlija, Damir, Young, Leonie S., Hamid, Anis A., Van Allen, Eliezer M., Sweeney, Christopher J., Gjini, Evisa, Lako, Ana, Hodi, F. Steven, Bellmunt, Joaquim, Brown, Myles, Cejas, Paloma, Long, Henry W.

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