MSIsensor: microsatellite instability detection using paired tumor-normal sequence data von Niu, Beifang, Ye, Kai, Zhang, Qunyuan, Lu, Charles, Xie, Mingchao, McLellan, Michael D, Wendl, Michael C, Ding, Li

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Mutational landscape and significance across 12 major cancer types von Kandoth, Cyriac, McLellan, Michael D., Vandin, Fabio, Ye, Kai, Niu, Beifang, Lu, Charles, Xie, Mingchao, Zhang, Qunyuan, McMichael, Joshua F., Wyczalkowski, Matthew A., Leiserson, Mark D. M., Miller, Christopher A., Welch, John S., Walter, Matthew J., Wendl, Michael C., Ley, Timothy J., Wilson, Richard K., Raphael, Benjamin J., Ding, Li

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VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing von Koboldt, Daniel C, Zhang, Qunyuan, Larson, David E, Shen, Dong, McLellan, Michael D, Lin, Ling, Miller, Christopher A, Mardis, Elaine R, Ding, Li, Wilson, Richard K

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VarScan: variant detection in massively parallel sequencing of individual and pooled samples von Koboldt, Daniel C., Chen, Ken, Wylie, Todd, Larson, David E., McLellan, Michael D., Mardis, Elaine R., Weinstock, George M., Wilson, Richard K., Ding, Li

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Clonal Architecture of Secondary Acute Myeloid Leukemia von Walter, Matthew J, Shen, Dong, Ding, Li, Shao, Jin, Koboldt, Daniel C, Chen, Ken, Larson, David E, McLellan, Michael D, Dooling, David, Abbott, Rachel, Fulton, Robert, Magrini, Vincent, Schmidt, Heather, Kalicki-Veizer, Joelle, O'Laughlin, Michelle, Fan, Xian, Grillot, Marcus, Witowski, Sarah, Heath, Sharon, Frater, John L, Eades, William, Tomasson, Michael, Westervelt, Peter, DiPersio, John F, Link, Daniel C, Mardis, Elaine R, Ley, Timothy J, Wilson, Richard K, Graubert, Timothy A

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Protein-structure-guided discovery of functional mutations across 19 cancer types von Niu, Beifang, Scott, Adam D, Sengupta, Sohini, Bailey, Matthew H, Batra, Prag, Ning, Jie, Wyczalkowski, Matthew A, Liang, Wen-Wei, Zhang, Qunyuan, McLellan, Michael D, Sun, Sam Q, Tripathi, Piyush, Lou, Carolyn, Ye, Kai, Mashl, R Jay, Wallis, John, Wendl, Michael C, Chen, Feng, Ding, Li

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BreakDancer: an algorithm for high-resolution mapping of genomic structural variation von Chen, Ken, Wallis, John W, McLellan, Michael D, Larson, David E, Kalicki, Joelle M, Pohl, Craig S, McGrath, Sean D, Wendl, Michael C, Zhang, Qunyuan, Locke, Devin P, Shi, Xiaoqi, Fulton, Robert S, Ley, Timothy J, Wilson, Richard K, Ding, Li, Mardis, Elaine R

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Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes von Graubert, Timothy A, Shen, Dong, Ding, Li, Okeyo-Owuor, Theresa, Lunn, Cara L, Shao, Jin, Krysiak, Kilannin, Harris, Christopher C, Koboldt, Daniel C, Larson, David E, McLellan, Michael D, Dooling, David J, Abbott, Rachel M, Fulton, Robert S, Schmidt, Heather, Kalicki-Veizer, Joelle, O'Laughlin, Michelle, Grillot, Marcus, Baty, Jack, Heath, Sharon, Frater, John L, Nasim, Talat, Link, Daniel C, Tomasson, Michael H, Westervelt, Peter, DiPersio, John F, Mardis, Elaine R, Ley, Timothy J, Wilson, Richard K, Walter, Matthew J

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Integrated analysis of germline and somatic variants in ovarian cancer von Kanchi, Krishna L., Johnson, Kimberly J., Lu, Charles, McLellan, Michael D., Leiserson, Mark D. M., Wendl, Michael C., Zhang, Qunyuan, Koboldt, Daniel C., Xie, Mingchao, Kandoth, Cyriac, McMichael, Joshua F., Wyczalkowski, Matthew A., Larson, David E., Schmidt, Heather K., Miller, Christopher A., Fulton, Robert S., Spellman, Paul T., Mardis, Elaine R., Druley, Todd E., Graubert, Timothy A., Goodfellow, Paul J., Raphael, Benjamin J., Wilson, Richard K., Ding, Li

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Systematic discovery of complex insertions and deletions in human cancers von Ye, Kai, Wang, Jiayin, Jayasinghe, Reyka, Lameijer, Eric-Wubbo, McMichael, Joshua F, Ning, Jie, McLellan, Michael D, Xie, Mingchao, Cao, Song, Yellapantula, Venkata, Huang, Kuan-lin, Scott, Adam, Foltz, Steven, Niu, Beifang, Johnson, Kimberly J, Moed, Matthijs, Slagboom, P Eline, Chen, Feng, Wendl, Michael C, Ding, Li

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An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer von Ruggles, Kelly V., Tang, Zuojian, Wang, Xuya, Grover, Himanshu, Askenazi, Manor, Teubl, Jennifer, Cao, Song, McLellan, Michael D., Clauser, Karl R., Tabb, David L., Mertins, Philipp, Slebos, Robbert, Erdmann-Gilmore, Petra, Li, Shunqiang, Gunawardena, Harsha P., Xie, Ling, Liu, Tao, Zhou, Jian-Ying, Sun, Shisheng, Hoadley, Katherine A., Perou, Charles M., Chen, Xian, Davies, Sherri R., Maher, Christopher A., Kinsinger, Christopher R., Rodland, Karen D., Zhang, Hui, Zhang, Zhen, Ding, Li, Townsend, R. Reid, Rodriguez, Henry, Chan, Daniel, Smith, Richard D., Liebler, Daniel C., Carr, Steven A., Payne, Samuel, Ellis, Matthew J., Fenyő, David

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Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif von Hamilton, Mark P., Rajapakshe, Kimal, Hartig, Sean M., Reva, Boris, McLellan, Michael D., Kandoth, Cyriac, Ding, Li, Zack, Travis I., Gunaratne, Preethi H., Wheeler, David A., Coarfa, Cristian, McGuire, Sean E.

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Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma von Gutmann, David H, McLellan, Michael D, Hussain, Ibrahim, Wallis, John W, Fulton, Lucinda L, Fulton, Robert S, Magrini, Vincent, Demeter, Ryan, Wylie, Todd, Kandoth, Cyriac, Leonard, Jeffrey R, Guha, Abhijit, Miller, Christopher A, Ding, Li, Mardis, Elaine R

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Optimized polyepitope neoantigen DNA vaccines elicit neoantigen-specific immune responses in preclinical models and in clinical translation von Li, Lijin, Zhang, Xiuli, Wang, Xiaoli, Kim, Samuel W., Herndon, John M., Becker-Hapak, Michelle K., Carreno, Beatriz M., Myers, Nancy B., Sturmoski, Mark A., McLellan, Michael D., Miller, Christopher A., Johanns, Tanner M., Tan, Benjamin R., Dunn, Gavin P., Fleming, Timothy P., Hansen, Ted H., Goedegebuure, S. Peter, Gillanders, William E.

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Novel MEK1 mutation identified by mutational analysis of epidermal growth factor receptor signaling pathway genes in lung adenocarcinoma von Marks, Jenifer L, Gong, Yixuan, Chitale, Dhananjay, Golas, Ben, McLellan, Michael D, Kasai, Yumi, Ding, Li, Mardis, Elaine R, Wilson, Richard K, Solit, David, Levine, Ross, Michel, Kathrin, Thomas, Roman K, Rusch, Valerie W, Ladanyi, Marc, Pao, William

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Neoantigen DNA vaccines are safe, feasible, and induce neoantigen-specific immune responses in triple-negative breast cancer patients von Zhang, Xiuli, Goedegebuure, S. Peter, Chen, Michael Y., Mishra, Rashmi, Zhang, Felicia, Yu, Yik Yeung, Singhal, Kartik, Li, Lijin, Gao, Feng, Myers, Nancy B., Vickery, Tammi, Hundal, Jasreet, McLellan, Michael D., Sturmoski, Mark A., Kim, Samuel W., Chen, Ina, Davidson, Jesse T., Sankpal, Narendra V., Myles, Stephanie, Suresh, Rama, Ma, Cynthia X., Foluso, Ademuyiwa, Wang-Gillam, Andrea, Davies, Sherri, Hagemann, Ian S., Mardis, Elaine R., Griffith, Obi, Griffith, Malachi, Miller, Christopher A., Hansen, Ted H., Fleming, Timothy P., Schreiber, Robert D., Gillanders, William E.

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Re-sequencing expands our understanding of the phenotypic impact of variants at GWAS loci von Service, Susan K, Teslovich, Tanya M, Fuchsberger, Christian, Ramensky, Vasily, Yajnik, Pranav, Koboldt, Daniel C, Larson, David E, Zhang, Qunyuan, Lin, Ling, Welch, Ryan, Ding, Li, McLellan, Michael D, O'Laughlin, Michele, Fronick, Catrina, Fulton, Lucinda L, Magrini, Vincent, Swift, Amy, Elliott, Paul, Jarvelin, Marjo-Riitta, Kaakinen, Marika, McCarthy, Mark I, Peltonen, Leena, Pouta, Anneli, Bonnycastle, Lori L, Collins, Francis S, Narisu, Narisu, Stringham, Heather M, Tuomilehto, Jaakko, Ripatti, Samuli, Fulton, Robert S, Sabatti, Chiara, Wilson, Richard K, Boehnke, Michael, Freimer, Nelson B

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BreakPoint Surveyor: a pipeline for structural variant visualization von Wyczalkowski, Matthew A, Wylie, Kristine M, Cao, Song, McLellan, Michael D, Flynn, Jennifer, Huang, Mo, Ye, Kai, Fan, Xian, Chen, Ken, Wendl, Michael C, Ding, Li

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HPV transcript expression affects cervical cancer response to chemoradiation von Ruiz, Fiona J., Inkman, Matthew, Rashmi, Ramachandran, Muhammad, Naoshad, Gabriel, Nishanth, Miller, Christopher A., McLellan, Michael D., Goldstein, Michael, Markovina, Stephanie, Grigsby, Perry W., Zhang, Jin, Schwarz, Julie K.

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Proteogenomics connects somatic mutations to signalling in breast cancer von Mertins, Philipp, Mani, D. R., Ruggles, Kelly V., Gillette, Michael A., Clauser, Karl R., Wang, Pei, Wang, Xianlong, Qiao, Jana W., Cao, Song, Petralia, Francesca, Kawaler, Emily, Mundt, Filip, Krug, Karsten, Tu, Zhidong, Lei, Jonathan T., Gatza, Michael L., Wilkerson, Matthew, Perou, Charles M., Yellapantula, Venkata, Huang, Kuan-lin, Lin, Chenwei, McLellan, Michael D., Yan, Ping, Davies, Sherri R., Townsend, R. Reid, Skates, Steven J., Wang, Jing, Zhang, Bing, Kinsinger, Christopher R., Mesri, Mehdi, Rodriguez, Henry, Ding, Li, Paulovich, Amanda G., Fenyö, David, Ellis, Matthew J., Carr, Steven A.

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