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Title: Systematic Analysis of Splice-Site-Creating Mutations in Cancer

Abstract

For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function. Notably, we found that neoantigens induced by SCMs are likely several folds more immunogenic compared to missense mutations, exemplified by the recurrent GATA3 SCM. Further, high expression of PD-1 and PD-L1 was observed in tumors with SCMs, suggesting candidates for immune blockade therapy. Finally, our work highlights the importance of integrating DNA and RNA data for understanding the functional and the clinical implications of mutations in human diseases.

Authors:
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  1. (Julia)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
Contributing Org.:
The Cancer Genome Atlas Research Network
OSTI Identifier:
1433509
Grant/Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Cell Reports
Additional Journal Information:
Journal Volume: 23; Journal Issue: 1; Journal ID: ISSN 2211-1247
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; splicing; RNA; mutations of clinical relevance

Citation Formats

Jayasinghe, Reyka G., Cao, Song, Gao, Qingsong, Wendl, Michael C., Vo, Nam Sy, Reynolds, Sheila M., Zhao, Yanyan, Climente-González, Héctor, Chai, Shengjie, Wang, Fang, Varghese, Rajees, Huang, Mo, Liang, Wen-Wei, Wyczalkowski, Matthew A., Sengupta, Sohini, Li, Zhi, Payne, Samuel H., Fenyö, David, Miner, Jeffrey H., Walter, Matthew J., Vincent, Benjamin, Eyras, Eduardo, Chen, Ken, Shmulevich, Ilya, Chen, Feng, Ding, Li, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan, Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. Onur, Sun, Yichao, Taylor, Barry S., Wang, Jioajiao, Zhang, Hongxin, Anur, Pavana, Peto, Myron, Spellman, Paul, Benz, Christopher, Stuart, Joshua M., Wong, Christopher K., Yau, Christina, Hayes, D. Neil, Parker, Joel S., Wilkerson, Matthew D., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert, Jones, Steven J. M., Kasaian, Katayoon, Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen, Robertson, A. Gordon, Sadeghi, Sara, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Berger, Ashton C., Beroukhim, Rameen, Cherniack, Andrew D., Cibulskis, Carrie, Gabriel, Stacey B., Gao, Galen F., Ha, Gavin, Meyerson, Matthew, Schumacher, Steven E., Shih, Juliann, Kucherlapati, Melanie H., Kucherlapati, Raju S., Baylin, Stephen, Cope, Leslie, Danilova, Ludmila, Bootwalla, Moiz S., Lai, Phillip H., Maglinte, Dennis T., Van Den Berg, David J., Weisenberger, Daniel J., Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Fan, Cheng, Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Perou, Amy H., Perou, Charles M., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Skelly, Tara, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Fan, Huihui, Hinoue, Toshinori, Laird, Peter W., Shen, Hui, Zhou, Wanding, Bellair, Michelle, Chang, Kyle, Covington, Kyle, Creighton, Chad J., Dinh, Huyen, Doddapaneni, HarshaVardhan, Donehower, Lawrence A., Drummond, Jennifer, Gibbs, Richard A., Glenn, Robert, Hale, Walker, Han, Yi, Hu, Jianhong, Korchina, Viktoriya, Lee, Sandra, Lewis, Lora, Li, Wei, Liu, Xiuping, Morgan, Margaret, Morton, Donna, Muzny, Donna, Santibanez, Jireh, Sheth, Margi, Shinbrot, Eve, Wang, Linghua, Wang, Min, Wheeler, David A., Xi, Liu, Zhao, Fengmei, Hess, Julian, Appelbaum, Elizabeth L., Bailey, Matthew, Cordes, Matthew G., Ding, Li, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Kandoth, Cyriac, Mardis, Elaine R., McLellan, Michael D., Miller, Christopher A., Schmidt, Heather K., Wilson, Richard K., Crain, Daniel, Curley, Erin, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Corcoran, Niall, Costello, Tony, Hovens, Christopher, Carvalho, Andre L., de Carvalho, Ana C., Fregnani, José H., Longatto-Filho, Adhemar, Reis, Rui M., Scapulatempo-Neto, Cristovam, Silveira, Henrique C. S., Vidal, Daniel O., Burnette, Andrew, Eschbacher, Jennifer, Hermes, Beth, Noss, Ardene, Singh, Rosy, Anderson, Matthew L., Castro, Patricia D., Ittmann, Michael, Huntsman, David, Kohl, Bernard, Le, Xuan, Thorp, Richard, Andry, Chris, Duffy, Elizabeth R., Lyadov, Vladimir, Paklina, Oxana, Setdikova, Galiya, Shabunin, Alexey, Tavobilov, Mikhail, McPherson, Christopher, Warnick, Ronald, Berkowitz, Ross, Cramer, Daniel, Feltmate, Colleen, Horowitz, Neil, Kibel, Adam, Muto, Michael, Raut, Chandrajit P., Malykh, Andrei, Barnholtz-Sloan, Jill S., Barrett, Wendi, Devine, Karen, Fulop, Jordonna, Ostrom, Quinn T., Shimmel, Kristen, Wolinsky, Yingli, Sloan, Andrew E., De Rose, Agostino, Giuliante, Felice, Goodman, Marc, Karlan, Beth Y., Hagedorn, Curt H., Eckman, John, Harr, Jodi, Myers, Jerome, Tucker, Kelinda, Zach, Leigh Anne, Deyarmin, Brenda, Hu, Hai, Kvecher, Leonid, Larson, Caroline, Mural, Richard J., Somiari, Stella, Vicha, Ales, Zelinka, Tomas, Bennett, Joseph, Iacocca, Mary, Rabeno, Brenda, Swanson, Patricia, Latour, Mathieu, Lacombe, Louis, Têtu, Bernard, Bergeron, Alain, McGraw, Mary, Staugaitis, Susan M., Chabot, John, Hibshoosh, Hanina, Sepulveda, Antonia, Su, Tao, Wang, Timothy, Potapova, Olga, Voronina, Olga, Desjardins, Laurence, Mariani, Odette, Roman-Roman, Sergio, Sastre, Xavier, Stern, Marc-Henri, Cheng, Feixiong, Signoretti, Sabina, Berchuck, Andrew, Bigner, Darell, Lipp, Eric, Marks, Jeffrey, McCall, Shannon, McLendon, Roger, Secord, Angeles, Sharp, Alexis, Behera, Madhusmita, Brat, Daniel J., Chen, Amy, Delman, Keith, Force, Seth, Khuri, Fadlo, Magliocca, Kelly, Maithel, Shishir, Olson, Jeffrey J., Owonikoko, Taofeek, Pickens, Alan, Ramalingam, Suresh, Shin, Dong M., Sica, Gabriel, Van Meir, Erwin G., Zhang, Hongzheng, Eijckenboom, Wil, Gillis, Ad, Korpershoek, Esther, Looijenga, Leendert, Oosterhuis, Wolter, Stoop, Hans, van Kessel, Kim E., Zwarthoff, Ellen C., Calatozzolo, Chiara, Cuppini, Lucia, Cuzzubbo, Stefania, DiMeco, Francesco, Finocchiaro, Gaetano, Mattei, Luca, Perin, Alessandro, Pollo, Bianca, Chen, Chu, Houck, John, Lohavanichbutr, Pawadee, Hartmann, Arndt, Stoehr, Christine, Stoehr, Robert, Taubert, Helge, Wach, Sven, Wullich, Bernd, Kycler, Witold, Murawa, Dawid, Wiznerowicz, Maciej, Chung, Ki, Edenfield, W. Jeffrey, Martin, Julie, Baudin, Eric, Bubley, Glenn, Bueno, Raphael, De Rienzo, Assunta, Richards, William G., Kalkanis, Steven, Mikkelsen, Tom, Noushmehr, Houtan, Scarpace, Lisa, Girard, Nicolas, Aymerich, Marta, Campo, Elias, Giné, Eva, Guillermo, Armando López, Van Bang, Nguyen, Hanh, Phan Thi, Phu, Bui Duc, Tang, Yufang, Colman, Howard, Evason, Kimberley, Dottino, Peter R., Martignetti, John A., Gabra, Hani, Juhl, Hartmut, Akeredolu, Teniola, Stepa, Serghei, Hoon, Dave, Ahn, Keunsoo, Kang, Koo Jeong, Beuschlein, Felix, Breggia, Anne, Birrer, Michael, Bell, Debra, Borad, Mitesh, Bryce, Alan H., Castle, Erik, Chandan, Vishal, Cheville, John, Copland, John A., Farnell, Michael, Flotte, Thomas, Giama, Nasra, Ho, Thai, Kendrick, Michael, Kocher, Jean-Pierre, Kopp, Karla, Moser, Catherine, Nagorney, David, O’Brien, Daniel, O’Neill, Brian Patrick, Patel, Tushar, Petersen, Gloria, Que, Florencia, Rivera, Michael, Roberts, Lewis, Smallridge, Robert, Smyrk, Thomas, Stanton, Melissa, Thompson, R. Houston, Torbenson, Michael, Yang, Ju Dong, Zhang, Lizhi, Brimo, Fadi, Ajani, Jaffer A., Gonzalez, Ana Maria Angulo, Behrens, Carmen, Bondaruk, Jolanta, Broaddus, Russell, Czerniak, Bogdan, Esmaeli, Bita, Fujimoto, Junya, Gershenwald, Jeffrey, Guo, Charles, Lazar, Alexander J., Logothetis, Christopher, Meric-Bernstam, Funda, Moran, Cesar, Ramondetta, Lois, Rice, David, Sood, Anil, Tamboli, Pheroze, Thompson, Timothy, Troncoso, Patricia, Tsao, Anne, Wistuba, Ignacio, Carter, Candace, Haydu, Lauren, Hersey, Peter, Jakrot, Valerie, Kakavand, Hojabr, Kefford, Richard, Lee, Kenneth, Long, Georgina, Mann, Graham, Quinn, Michael, Saw, Robyn, Scolyer, Richard, Shannon, Kerwin, Spillane, Andrew, Stretch, Jonathan, Synott, Maria, Thompson, John, Wilmott, James, Al-Ahmadie, Hikmat, Chan, Timothy A., Ghossein, Ronald, Gopalan, Anuradha, Levine, Douglas A., Reuter, Victor, Singer, Samuel, Singh, Bhuvanesh, Tien, Nguyen Viet, Broudy, Thomas, Mirsaidi, Cyrus, Nair, Praveen, Drwiega, Paul, Miller, Judy, Smith, Jennifer, Zaren, Howard, Park, Joong-Won, Hung, Nguyen Phi, Kebebew, Electron, Linehan, W. Marston, Metwalli, Adam R., Pacak, Karel, Pinto, Peter A., Schiffman, Mark, Schmidt, Laura S., Vocke, Cathy D., Wentzensen, Nicolas, Worrell, Robert, Yang, Hannah, Moncrieff, Marc, Goparaju, Chandra, Melamed, Jonathan, Pass, Harvey, Botnariuc, Natalia, Caraman, Irina, Cernat, Mircea, Chemencedji, Inga, Clipca, Adrian, Doruc, Serghei, Gorincioi, Ghenadie, Mura, Sergiu, Pirtac, Maria, Stancul, Irina, Tcaciuc, Diana, Albert, Monique, Alexopoulou, Iakovina, Arnaout, Angel, Bartlett, John, Engel, Jay, Gilbert, Sebastien, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Rassl, Doris M., Rintoul, Robert C., Bifulco, Carlo, Tamakawa, Raina, Urba, Walter, Hayward, Nicholas, Timmers, Henri, Antenucci, Anna, Facciolo, Francesco, Grazi, Gianluca, Marino, Mirella, Merola, Roberta, de Krijger, Ronald, Gimenez-Roqueplo, Anne-Paule, Piché, Alain, Chevalier, Simone, McKercher, Ginette, Birsoy, Kivanc, Barnett, Gene, Brewer, Cathy, Farver, Carol, Naska, Theresa, Pennell, Nathan A., Raymond, Daniel, Schilero, Cathy, Smolenski, Kathy, Williams, Felicia, Morrison, Carl, Borgia, Jeffrey A., Liptay, Michael J., Pool, Mark, Seder, Christopher W., Junker, Kerstin, Omberg, Larsson, Dinkin, Mikhail, Manikhas, George, Alvaro, Domenico, Bragazzi, Maria Consiglia, Cardinale, Vincenzo, Carpino, Guido, Gaudio, Eugenio, Chesla, David, Cottingham, Sandra, Dubina, Michael, Moiseenko, Fedor, Dhanasekaran, Renumathy, Becker, Karl-Friedrich, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Abdel-Rahman, Mohamed H., Aziz, Dina, Bell, Sue, Cebulla, Colleen M., Davis, Amy, Duell, Rebecca, Elder, J. Bradley, Hilty, Joe, Kumar, Bahavna, Lang, James, Lehman, Norman L., Mandt, Randy, Nguyen, Phuong, Pilarski, Robert, Rai, Karan, Schoenfield, Lynn, Senecal, Kelly, Wakely, Paul, Hansen, Paul, Lechan, Ronald, Powers, James, Tischler, Arthur, Grizzle, William E., Sexton, Katherine C., Kastl, Alison, Henderson, Joel, Porten, Sima, Waldmann, Jens, Fassnacht, Martin, Asa, Sylvia L., Schadendorf, Dirk, Couce, Marta, Graefen, Markus, Huland, Hartwig, Sauter, Guido, Schlomm, Thorsten, Simon, Ronald, Tennstedt, Pierre, Olabode, Oluwole, Nelson, Mark, Bathe, Oliver, Carroll, Peter R., Chan, June M., Disaia, Philip, Glenn, Pat, Kelley, Robin K., Landen, Charles N., Phillips, Joanna, Prados, Michael, Simko, Jeffry, Smith-McCune, Karen, VandenBerg, Scott, Roggin, Kevin, Fehrenbach, Ashley, Kendler, Ady, Sifri, Suzanne, Steele, Ruth, Jimeno, Antonio, Carey, Francis, Forgie, Ian, Mannelli, Massimo, Carney, Michael, Hernandez, Brenda, Campos, Benito, Herold-Mende, Christel, Jungk, Christin, Unterberg, Andreas, von Deimling, Andreas, Bossler, Aaron, Galbraith, Joseph, Jacobus, Laura, Knudson, Michael, Knutson, Tina, Ma, Deqin, Milhem, Mohammed, Sigmund, Rita, Godwin, Andrew K., Madan, Rashna, Rosenthal, Howard G., Adebamowo, Clement, Adebamowo, Sally N., Boussioutas, Alex, Beer, David, Giordano, Thomas, Mes-Masson, Anne-Marie, Saad, Fred, Bocklage, Therese, Landrum, Lisa, Mannel, Robert, Moore, Kathleen, Moxley, Katherine, Postier, Russel, Walker, Joan, Zuna, Rosemary, Feldman, Michael, Valdivieso, Federico, Dhir, Rajiv, Luketich, James, Pinero, Edna M. 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Jayasinghe, Reyka G., Cao, Song, Gao, Qingsong, Wendl, Michael C., Vo, Nam Sy, Reynolds, Sheila M., Zhao, Yanyan, Climente-González, Héctor, Chai, Shengjie, Wang, Fang, Varghese, Rajees, Huang, Mo, Liang, Wen-Wei, Wyczalkowski, Matthew A., Sengupta, Sohini, Li, Zhi, Payne, Samuel H., Fenyö, David, Miner, Jeffrey H., Walter, Matthew J., Vincent, Benjamin, Eyras, Eduardo, Chen, Ken, Shmulevich, Ilya, Chen, Feng, Ding, Li, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan, Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. Onur, Sun, Yichao, Taylor, Barry S., Wang, Jioajiao, Zhang, Hongxin, Anur, Pavana, Peto, Myron, Spellman, Paul, Benz, Christopher, Stuart, Joshua M., Wong, Christopher K., Yau, Christina, Hayes, D. Neil, Parker, Joel S., Wilkerson, Matthew D., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert, Jones, Steven J. M., Kasaian, Katayoon, Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen, Robertson, A. Gordon, Sadeghi, Sara, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Berger, Ashton C., Beroukhim, Rameen, Cherniack, Andrew D., Cibulskis, Carrie, Gabriel, Stacey B., Gao, Galen F., Ha, Gavin, Meyerson, Matthew, Schumacher, Steven E., Shih, Juliann, Kucherlapati, Melanie H., Kucherlapati, Raju S., Baylin, Stephen, Cope, Leslie, Danilova, Ludmila, Bootwalla, Moiz S., Lai, Phillip H., Maglinte, Dennis T., Van Den Berg, David J., Weisenberger, Daniel J., Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Fan, Cheng, Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Perou, Amy H., Perou, Charles M., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Skelly, Tara, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Fan, Huihui, Hinoue, Toshinori, Laird, Peter W., Shen, Hui, Zhou, Wanding, Bellair, Michelle, Chang, Kyle, Covington, Kyle, Creighton, Chad J., Dinh, Huyen, Doddapaneni, HarshaVardhan, Donehower, Lawrence A., Drummond, Jennifer, Gibbs, Richard A., Glenn, Robert, Hale, Walker, Han, Yi, Hu, Jianhong, Korchina, Viktoriya, Lee, Sandra, Lewis, Lora, Li, Wei, Liu, Xiuping, Morgan, Margaret, Morton, Donna, Muzny, Donna, Santibanez, Jireh, Sheth, Margi, Shinbrot, Eve, Wang, Linghua, Wang, Min, Wheeler, David A., Xi, Liu, Zhao, Fengmei, Hess, Julian, Appelbaum, Elizabeth L., Bailey, Matthew, Cordes, Matthew G., Ding, Li, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Kandoth, Cyriac, Mardis, Elaine R., McLellan, Michael D., Miller, Christopher A., Schmidt, Heather K., Wilson, Richard K., Crain, Daniel, Curley, Erin, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Corcoran, Niall, Costello, Tony, Hovens, Christopher, Carvalho, Andre L., de Carvalho, Ana C., Fregnani, José H., Longatto-Filho, Adhemar, Reis, Rui M., Scapulatempo-Neto, Cristovam, Silveira, Henrique C. 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@article{osti_1433509,
title = {Systematic Analysis of Splice-Site-Creating Mutations in Cancer},
author = {Jayasinghe, Reyka G. and Cao, Song and Gao, Qingsong and Wendl, Michael C. and Vo, Nam Sy and Reynolds, Sheila M. and Zhao, Yanyan and Climente-González, Héctor and Chai, Shengjie and Wang, Fang and Varghese, Rajees and Huang, Mo and Liang, Wen-Wei and Wyczalkowski, Matthew A. and Sengupta, Sohini and Li, Zhi and Payne, Samuel H. and Fenyö, David and Miner, Jeffrey H. and Walter, Matthew J. and Vincent, Benjamin and Eyras, Eduardo and Chen, Ken and Shmulevich, Ilya and Chen, Feng and Ding, Li and Caesar-Johnson, Samantha J. and Demchok, John A. and Felau, Ina and Kasapi, Melpomeni and Ferguson, Martin L. and Hutter, Carolyn M. and Sofia, Heidi J. and Tarnuzzer, Roy and Wang, Zhining and Yang, Liming and Zenklusen, Jean C. and Zhang, Jiashan and Chudamani, Sudha and Liu, Jia and Lolla, Laxmi and Naresh, Rashi and Pihl, Todd and Sun, Qiang and Wan, Yunhu and Wu, Ye and Cho, Juok and DeFreitas, Timothy and Frazer, Scott and Gehlenborg, Nils and Getz, Gad and Heiman, David I. and Kim, Jaegil and Lawrence, Michael S. and Lin, Pei and Meier, Sam and Noble, Michael S. and Saksena, Gordon and Voet, Doug and Zhang, Hailei and Bernard, Brady and Chambwe, Nyasha and Dhankani, Varsha and Knijnenburg, Theo and Kramer, Roger and Leinonen, Kalle and Liu, Yuexin and Miller, Michael and Reynolds, Sheila and Shmulevich, Ilya and Thorsson, Vesteinn and Zhang, Wei and Akbani, Rehan and Broom, Bradley M. and Hegde, Apurva M. and Ju, Zhenlin and Kanchi, Rupa S. and Korkut, Anil and Li, Jun and Liang, Han and Ling, Shiyun and Liu, Wenbin and Lu, Yiling and Mills, Gordon B. and Ng, Kwok-Shing and Rao, Arvind and Ryan, Michael and Wang, Jing and Weinstein, John N. and Zhang, Jiexin and Abeshouse, Adam and Armenia, Joshua and Chakravarty, Debyani and Chatila, Walid K. and de Bruijn, Ino and Gao, Jianjiong and Gross, Benjamin E. and Heins, Zachary J. and Kundra, Ritika and La, Konnor and Ladanyi, Marc and Luna, Augustin and Nissan, Moriah G. and Ochoa, Angelica and Phillips, Sarah M. and Reznik, Ed and Sanchez-Vega, Francisco and Sander, Chris and Schultz, Nikolaus and Sheridan, Robert and Sumer, S. Onur and Sun, Yichao and Taylor, Barry S. and Wang, Jioajiao and Zhang, Hongxin and Anur, Pavana and Peto, Myron and Spellman, Paul and Benz, Christopher and Stuart, Joshua M. and Wong, Christopher K. and Yau, Christina and Hayes, D. Neil and Parker, Joel S. and Wilkerson, Matthew D. and Ally, Adrian and Balasundaram, Miruna and Bowlby, Reanne and Brooks, Denise and Carlsen, Rebecca and Chuah, Eric and Dhalla, Noreen and Holt, Robert and Jones, Steven J. M. and Kasaian, Katayoon and Lee, Darlene and Ma, Yussanne and Marra, Marco A. and Mayo, Michael and Moore, Richard A. and Mungall, Andrew J. and Mungall, Karen and Robertson, A. Gordon and Sadeghi, Sara and Schein, Jacqueline E. and Sipahimalani, Payal and Tam, Angela and Thiessen, Nina and Tse, Kane and Wong, Tina and Berger, Ashton C. and Beroukhim, Rameen and Cherniack, Andrew D. and Cibulskis, Carrie and Gabriel, Stacey B. and Gao, Galen F. and Ha, Gavin and Meyerson, Matthew and Schumacher, Steven E. and Shih, Juliann and Kucherlapati, Melanie H. and Kucherlapati, Raju S. and Baylin, Stephen and Cope, Leslie and Danilova, Ludmila and Bootwalla, Moiz S. and Lai, Phillip H. and Maglinte, Dennis T. and Van Den Berg, David J. and Weisenberger, Daniel J. and Auman, J. Todd and Balu, Saianand and Bodenheimer, Tom and Fan, Cheng and Hoadley, Katherine A. and Hoyle, Alan P. and Jefferys, Stuart R. and Jones, Corbin D. and Meng, Shaowu and Mieczkowski, Piotr A. and Mose, Lisle E. and Perou, Amy H. and Perou, Charles M. and Roach, Jeffrey and Shi, Yan and Simons, Janae V. and Skelly, Tara and Soloway, Matthew G. and Tan, Donghui and Veluvolu, Umadevi and Fan, Huihui and Hinoue, Toshinori and Laird, Peter W. and Shen, Hui and Zhou, Wanding and Bellair, Michelle and Chang, Kyle and Covington, Kyle and Creighton, Chad J. and Dinh, Huyen and Doddapaneni, HarshaVardhan and Donehower, Lawrence A. and Drummond, Jennifer and Gibbs, Richard A. and Glenn, Robert and Hale, Walker and Han, Yi and Hu, Jianhong and Korchina, Viktoriya and Lee, Sandra and Lewis, Lora and Li, Wei and Liu, Xiuping and Morgan, Margaret and Morton, Donna and Muzny, Donna and Santibanez, Jireh and Sheth, Margi and Shinbrot, Eve and Wang, Linghua and Wang, Min and Wheeler, David A. and Xi, Liu and Zhao, Fengmei and Hess, Julian and Appelbaum, Elizabeth L. and Bailey, Matthew and Cordes, Matthew G. and Ding, Li and Fronick, Catrina C. and Fulton, Lucinda A. and Fulton, Robert S. and Kandoth, Cyriac and Mardis, Elaine R. and McLellan, Michael D. and Miller, Christopher A. and Schmidt, Heather K. and Wilson, Richard K. and Crain, Daniel and Curley, Erin and Gardner, Johanna and Lau, Kevin and Mallery, David and Morris, Scott and Paulauskis, Joseph and Penny, Robert and Shelton, Candace and Shelton, Troy and Sherman, Mark and Thompson, Eric and Yena, Peggy and Bowen, Jay and Gastier-Foster, Julie M. and Gerken, Mark and Leraas, Kristen M. and Lichtenberg, Tara M. and Ramirez, Nilsa C. and Wise, Lisa and Zmuda, Erik and Corcoran, Niall and Costello, Tony and Hovens, Christopher and Carvalho, Andre L. and de Carvalho, Ana C. and Fregnani, José H. and Longatto-Filho, Adhemar and Reis, Rui M. and Scapulatempo-Neto, Cristovam and Silveira, Henrique C. S. and Vidal, Daniel O. and Burnette, Andrew and Eschbacher, Jennifer and Hermes, Beth and Noss, Ardene and Singh, Rosy and Anderson, Matthew L. and Castro, Patricia D. and Ittmann, Michael and Huntsman, David and Kohl, Bernard and Le, Xuan and Thorp, Richard and Andry, Chris and Duffy, Elizabeth R. and Lyadov, Vladimir and Paklina, Oxana and Setdikova, Galiya and Shabunin, Alexey and Tavobilov, Mikhail and McPherson, Christopher and Warnick, Ronald and Berkowitz, Ross and Cramer, Daniel and Feltmate, Colleen and Horowitz, Neil and Kibel, Adam and Muto, Michael and Raut, Chandrajit P. and Malykh, Andrei and Barnholtz-Sloan, Jill S. and Barrett, Wendi and Devine, Karen and Fulop, Jordonna and Ostrom, Quinn T. and Shimmel, Kristen and Wolinsky, Yingli and Sloan, Andrew E. and De Rose, Agostino and Giuliante, Felice and Goodman, Marc and Karlan, Beth Y. and Hagedorn, Curt H. and Eckman, John and Harr, Jodi and Myers, Jerome and Tucker, Kelinda and Zach, Leigh Anne and Deyarmin, Brenda and Hu, Hai and Kvecher, Leonid and Larson, Caroline and Mural, Richard J. and Somiari, Stella and Vicha, Ales and Zelinka, Tomas and Bennett, Joseph and Iacocca, Mary and Rabeno, Brenda and Swanson, Patricia and Latour, Mathieu and Lacombe, Louis and Têtu, Bernard and Bergeron, Alain and McGraw, Mary and Staugaitis, Susan M. and Chabot, John and Hibshoosh, Hanina and Sepulveda, Antonia and Su, Tao and Wang, Timothy and Potapova, Olga and Voronina, Olga and Desjardins, Laurence and Mariani, Odette and Roman-Roman, Sergio and Sastre, Xavier and Stern, Marc-Henri and Cheng, Feixiong and Signoretti, Sabina and Berchuck, Andrew and Bigner, Darell and Lipp, Eric and Marks, Jeffrey and McCall, Shannon and McLendon, Roger and Secord, Angeles and Sharp, Alexis and Behera, Madhusmita and Brat, Daniel J. and Chen, Amy and Delman, Keith and Force, Seth and Khuri, Fadlo and Magliocca, Kelly and Maithel, Shishir and Olson, Jeffrey J. and Owonikoko, Taofeek and Pickens, Alan and Ramalingam, Suresh and Shin, Dong M. and Sica, Gabriel and Van Meir, Erwin G. and Zhang, Hongzheng and Eijckenboom, Wil and Gillis, Ad and Korpershoek, Esther and Looijenga, Leendert and Oosterhuis, Wolter and Stoop, Hans and van Kessel, Kim E. and Zwarthoff, Ellen C. and Calatozzolo, Chiara and Cuppini, Lucia and Cuzzubbo, Stefania and DiMeco, Francesco and Finocchiaro, Gaetano and Mattei, Luca and Perin, Alessandro and Pollo, Bianca and Chen, Chu and Houck, John and Lohavanichbutr, Pawadee and Hartmann, Arndt and Stoehr, Christine and Stoehr, Robert and Taubert, Helge and Wach, Sven and Wullich, Bernd and Kycler, Witold and Murawa, Dawid and Wiznerowicz, Maciej and Chung, Ki and Edenfield, W. 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Houston and Torbenson, Michael and Yang, Ju Dong and Zhang, Lizhi and Brimo, Fadi and Ajani, Jaffer A. and Gonzalez, Ana Maria Angulo and Behrens, Carmen and Bondaruk, Jolanta and Broaddus, Russell and Czerniak, Bogdan and Esmaeli, Bita and Fujimoto, Junya and Gershenwald, Jeffrey and Guo, Charles and Lazar, Alexander J. and Logothetis, Christopher and Meric-Bernstam, Funda and Moran, Cesar and Ramondetta, Lois and Rice, David and Sood, Anil and Tamboli, Pheroze and Thompson, Timothy and Troncoso, Patricia and Tsao, Anne and Wistuba, Ignacio and Carter, Candace and Haydu, Lauren and Hersey, Peter and Jakrot, Valerie and Kakavand, Hojabr and Kefford, Richard and Lee, Kenneth and Long, Georgina and Mann, Graham and Quinn, Michael and Saw, Robyn and Scolyer, Richard and Shannon, Kerwin and Spillane, Andrew and Stretch, Jonathan and Synott, Maria and Thompson, John and Wilmott, James and Al-Ahmadie, Hikmat and Chan, Timothy A. and Ghossein, Ronald and Gopalan, Anuradha and Levine, Douglas A. and Reuter, Victor and Singer, Samuel and Singh, Bhuvanesh and Tien, Nguyen Viet and Broudy, Thomas and Mirsaidi, Cyrus and Nair, Praveen and Drwiega, Paul and Miller, Judy and Smith, Jennifer and Zaren, Howard and Park, Joong-Won and Hung, Nguyen Phi and Kebebew, Electron and Linehan, W. Marston and Metwalli, Adam R. and Pacak, Karel and Pinto, Peter A. and Schiffman, Mark and Schmidt, Laura S. and Vocke, Cathy D. and Wentzensen, Nicolas and Worrell, Robert and Yang, Hannah and Moncrieff, Marc and Goparaju, Chandra and Melamed, Jonathan and Pass, Harvey and Botnariuc, Natalia and Caraman, Irina and Cernat, Mircea and Chemencedji, Inga and Clipca, Adrian and Doruc, Serghei and Gorincioi, Ghenadie and Mura, Sergiu and Pirtac, Maria and Stancul, Irina and Tcaciuc, Diana and Albert, Monique and Alexopoulou, Iakovina and Arnaout, Angel and Bartlett, John and Engel, Jay and Gilbert, Sebastien and Parfitt, Jeremy and Sekhon, Harman and Thomas, George and Rassl, Doris M. and Rintoul, Robert C. and Bifulco, Carlo and Tamakawa, Raina and Urba, Walter and Hayward, Nicholas and Timmers, Henri and Antenucci, Anna and Facciolo, Francesco and Grazi, Gianluca and Marino, Mirella and Merola, Roberta and de Krijger, Ronald and Gimenez-Roqueplo, Anne-Paule and Piché, Alain and Chevalier, Simone and McKercher, Ginette and Birsoy, Kivanc and Barnett, Gene and Brewer, Cathy and Farver, Carol and Naska, Theresa and Pennell, Nathan A. and Raymond, Daniel and Schilero, Cathy and Smolenski, Kathy and Williams, Felicia and Morrison, Carl and Borgia, Jeffrey A. and Liptay, Michael J. and Pool, Mark and Seder, Christopher W. and Junker, Kerstin and Omberg, Larsson and Dinkin, Mikhail and Manikhas, George and Alvaro, Domenico and Bragazzi, Maria Consiglia and Cardinale, Vincenzo and Carpino, Guido and Gaudio, Eugenio and Chesla, David and Cottingham, Sandra and Dubina, Michael and Moiseenko, Fedor and Dhanasekaran, Renumathy and Becker, Karl-Friedrich and Janssen, Klaus-Peter and Slotta-Huspenina, Julia and Abdel-Rahman, Mohamed H. and Aziz, Dina and Bell, Sue and Cebulla, Colleen M. and Davis, Amy and Duell, Rebecca and Elder, J. Bradley and Hilty, Joe and Kumar, Bahavna and Lang, James and Lehman, Norman L. and Mandt, Randy and Nguyen, Phuong and Pilarski, Robert and Rai, Karan and Schoenfield, Lynn and Senecal, Kelly and Wakely, Paul and Hansen, Paul and Lechan, Ronald and Powers, James and Tischler, Arthur and Grizzle, William E. and Sexton, Katherine C. and Kastl, Alison and Henderson, Joel and Porten, Sima and Waldmann, Jens and Fassnacht, Martin and Asa, Sylvia L. and Schadendorf, Dirk and Couce, Marta and Graefen, Markus and Huland, Hartwig and Sauter, Guido and Schlomm, Thorsten and Simon, Ronald and Tennstedt, Pierre and Olabode, Oluwole and Nelson, Mark and Bathe, Oliver and Carroll, Peter R. and Chan, June M. and Disaia, Philip and Glenn, Pat and Kelley, Robin K. and Landen, Charles N. and Phillips, Joanna and Prados, Michael and Simko, Jeffry and Smith-McCune, Karen and VandenBerg, Scott and Roggin, Kevin and Fehrenbach, Ashley and Kendler, Ady and Sifri, Suzanne and Steele, Ruth and Jimeno, Antonio and Carey, Francis and Forgie, Ian and Mannelli, Massimo and Carney, Michael and Hernandez, Brenda and Campos, Benito and Herold-Mende, Christel and Jungk, Christin and Unterberg, Andreas and von Deimling, Andreas and Bossler, Aaron and Galbraith, Joseph and Jacobus, Laura and Knudson, Michael and Knutson, Tina and Ma, Deqin and Milhem, Mohammed and Sigmund, Rita and Godwin, Andrew K. and Madan, Rashna and Rosenthal, Howard G. and Adebamowo, Clement and Adebamowo, Sally N. and Boussioutas, Alex and Beer, David and Giordano, Thomas and Mes-Masson, Anne-Marie and Saad, Fred and Bocklage, Therese and Landrum, Lisa and Mannel, Robert and Moore, Kathleen and Moxley, Katherine and Postier, Russel and Walker, Joan and Zuna, Rosemary and Feldman, Michael and Valdivieso, Federico and Dhir, Rajiv and Luketich, James and Pinero, Edna M. Mora and Quintero-Aguilo, Mario and Carlotti, Carlos Gilberto and Dos Santos, Jose Sebastião and Kemp, Rafael and Sankarankuty, Ajith and Tirapelli, Daniela and Catto, James and Agnew, Kathy and Swisher, Elizabeth and Creaney, Jenette and Robinson, Bruce and Shelley, Carl Simon and Godwin, Eryn M. and Kendall, Sara and Shipman, Cassaundra and Bradford, Carol and Carey, Thomas and Haddad, Andrea and Moyer, Jeffey and Peterson, Lisa and Prince, Mark and Rozek, Laura and Wolf, Gregory and Bowman, Rayleen and Fong, Kwun M. and Yang, Ian and Korst, Robert and Rathmell, W. Kimryn and Fantacone-Campbell, J. Leigh and Hooke, Jeffrey A. and Kovatich, Albert J. and Shriver, Craig D. and DiPersio, John and Drake, Bettina and Govindan, Ramaswamy and Heath, Sharon and Ley, Timothy and Van Tine, Brian and Westervelt, Peter and Rubin, Mark A. and Lee, Jung Il and Aredes, Natália D. and Mariamidze, Armaz},
abstractNote = {For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function. Notably, we found that neoantigens induced by SCMs are likely several folds more immunogenic compared to missense mutations, exemplified by the recurrent GATA3 SCM. Further, high expression of PD-1 and PD-L1 was observed in tumors with SCMs, suggesting candidates for immune blockade therapy. Finally, our work highlights the importance of integrating DNA and RNA data for understanding the functional and the clinical implications of mutations in human diseases.},
doi = {10.1016/J.CELREP.2018.03.052},
journal = {Cell Reports},
number = 1,
volume = 23,
place = {United States},
year = {Thu Apr 05 00:00:00 EDT 2018},
month = {Thu Apr 05 00:00:00 EDT 2018}
}

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