The Next-Generation Sequencing Revolution and Its Impact on Genomics von Koboldt, Daniel C., Steinberg, Karyn Meltz, Larson, David E., Wilson, Richard K., Mardis, Elaine R.

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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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CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer von Griffith, Malachi, Spies, Nicholas C, Krysiak, Kilannin, McMichael, Joshua F, Coffman, Adam C, Danos, Arpad M, Ainscough, Benjamin J, Ramirez, Cody A, Rieke, Damian T, Kujan, Lynzey, Barnell, Erica K, Wagner, Alex H, Skidmore, Zachary L, Wollam, Amber, Liu, Connor J, Jones, Martin R, Bilski, Rachel L, Lesurf, Robert, Feng, Yan-Yang, Shah, Nakul M, Bonakdar, Melika, Trani, Lee, Matlock, Matthew, Ramu, Avinash, Campbell, Katie M, Spies, Gregory C, Graubert, Aaron P, Gangavarapu, Karthik, Eldred, James M, Larson, David E, Walker, Jason R, Good, Benjamin M, Wu, Chunlei, Su, Andrew I, Dienstmann, Rodrigo, Margolin, Adam A, Tamborero, David, Lopez-Bigas, Nuria, Jones, Steven J M, Bose, Ron, Spencer, David H, Wartman, Lukas D, Wilson, Richard K, Mardis, Elaine R, Griffith, Obi L

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SomaticSniper: identification of somatic point mutations in whole genome sequencing data von Larson, David E., Harris, Christopher C., Chen, Ken, Koboldt, Daniel C., Abbott, Travis E., Dooling, David J., Ley, Timothy J., Mardis, Elaine R., Wilson, Richard K., Ding, Li

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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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Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects von Regier, Allison A., Farjoun, Yossi, Larson, David E., Krasheninina, Olga, Kang, Hyun Min, Howrigan, Daniel P., Chen, Bo-Juen, Kher, Manisha, Banks, Eric, Ames, Darren C., English, Adam C., Li, Heng, Xing, Jinchuan, Zhang, Yeting, Matise, Tara, Abecasis, Goncalo R., Salerno, Will, Zody, Michael C., Neale, Benjamin M., Hall, Ira M.

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The prognostic effects of somatic mutations in ER-positive breast cancer von Griffith, Obi L., Spies, Nicholas C., Anurag, Meenakshi, Griffith, Malachi, Luo, Jingqin, Tu, Dongsheng, Yeo, Belinda, Kunisaki, Jason, Miller, Christopher A, Krysiak, Kilannin, Hundal, Jasreet, Ainscough, Benjamin J, Skidmore, Zachary L., Campbell, Katie, Kumar, Runjun, Fronick, Catrina, Cook, Lisa, Snider, Jacqueline E., Davies, Sherri, Kavuri, Shyam M., Chang, Eric C., Magrini, Vincent, Larson, David E., Fulton, Robert S, Liu, Shuzhen, Leung, Samuel, Voduc, David, Bose, Ron, Dowsett, Mitch, Wilson, Richard K., Nielsen, Torsten O., Mardis, Elaine R, Ellis, Matthew J.

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Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection von Koboldt, Daniel C., Larson, David E., Wilson, Richard K.

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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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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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Background Mutations in Parental Cells Account for Most of the Genetic Heterogeneity of Induced Pluripotent Stem Cells von Young, Margaret A., Larson, David E., Sun, Chiao-Wang, George, Daniel R., Ding, Li, Miller, Christopher A., Lin, Ling, Pawlik, Kevin M., Chen, Ken, Fan, Xian, Schmidt, Heather, Kalicki-Veizer, Joelle, Cook, Lisa L., Swift, Gary W., Demeter, Ryan T., Wendl, Michael C., Sands, Mark S., Mardis, Elaine R., Wilson, Richard K., Townes, Tim M., Ley, Timothy J.

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Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers von Miller, Christopher A., Gindin, Yevgeniy, Lu, Charles, Griffith, Obi L, Griffith, Malachi, Shen, Dong, Hoog, Jeremy, Li, Tiandao, Larson, David E., Watson, Mark, Davies, Sherri R, Hunt, Kelly, Suman, Vera J., Snider, Jacqueline, Walsh, Thomas, Colditz, Graham A., DeSchryver, Katherine, Wilson, Richard K., Mardis, Elaine R., Ellis, Matthew J.

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Csk-Deficient Boundary Cells Are Eliminated from Normal Drosophila Epithelia by Exclusion, Migration, and Apoptosis von Vidal, Marcos, Larson, David E., Cagan, Ross L.

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Optimizing Cancer Genome Sequencing and Analysis von Griffith, Malachi, Miller, Christopher A., Griffith, Obi L., Krysiak, Kilannin, Skidmore, Zachary L., Ramu, Avinash, Walker, Jason R., Dang, Ha X., Trani, Lee, Larson, David E., Demeter, Ryan T., Wendl, Michael C., McMichael, Joshua F., Austin, Rachel E., Magrini, Vincent, McGrath, Sean D., Ly, Amy, Kulkarni, Shashikant, Cordes, Matthew G., Fronick, Catrina C., Fulton, Robert S., Maher, Christopher A., Ding, Li, Klco, Jeffery M., Mardis, Elaine R., Ley, Timothy J., Wilson, Richard K.

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Exome-Based Mapping and Variant Prioritization for Inherited Mendelian Disorders von Koboldt, Daniel C., Larson, David E., Sullivan, Lori S., Bowne, Sara J., Steinberg, Karyn M., Churchill, Jennifer D., Buhr, Aimee C., Nutter, Nathan, Pierce, Eric A., Blanton, Susan H., Weinstock, George M., Wilson, Richard K., Daiger, Stephen P.

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Truncating Prolactin Receptor Mutations Promote Tumor Growth in Murine Estrogen Receptor-Alpha Mammary Carcinomas von Griffith, Obi L., Chan, Szeman Ruby, Griffith, Malachi, Krysiak, Kilannin, Skidmore, Zachary L., Hundal, Jasreet, Allen, Julie A., Arthur, Cora D., Runci, Daniele, Bugatti, Mattia, Miceli, Alexander P., Schmidt, Heather, Trani, Lee, Kanchi, Krishna-Latha, Miller, Christopher A., Larson, David E., Fulton, Robert S., Vermi, William, Wilson, Richard K., Schreiber, Robert D., Mardis, Elaine R.

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The clonal evolution of metastatic colorectal cancer von Dang, Ha X., Krasnick, Bradley A., White, Brian S., Grossman, Julie G., Strand, Matthew S., Zhang, Jin, Cabanski, Christopher R., Miller, Christopher A., Fulton, Robert S., Goedegebuure, S. Peter, Fronick, Catrina C., Griffith, Malachi, Larson, David E., Goetz, Brian D., Walker, Jason R., Hawkins, William G., Strasberg, Steven M., Linehan, David C., Lim, Kian H., Lockhart, A. Craig, Mardis, Elaine R., Wilson, Richard K., Ley, Timothy J., Maher, Christopher A., Fields, Ryan C.

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Author Correction: The prognostic effects of somatic mutations in ER-positive breast cancer von Griffith, Obi L., Spies, Nicholas C., Anurag, Meenakshi, Griffith, Malachi, Luo, Jingqin, Tu, Dongsheng, Yeo, Belinda, Kunisaki, Jason, Miller, Christopher A, Krysiak, Kilannin, Hundal, Jasreet, Ainscough, Benjamin J, Skidmore, Zachary L., Campbell, Katie, Kumar, Runjun, Fronick, Catrina, Cook, Lisa, Snider, Jacqueline E., Davies, Sherri, Kavuri, Shyam M., Chang, Eric C., Magrini, Vincent, Larson, David E., Fulton, Robert S, Liu, Shuzhen, Leung, Samuel, Voduc, David, Bose, Ron, Dowsett, Mitch, Wilson, Richard K., Nielsen, Torsten O., Mardis, Elaine R, Ellis, Matthew J.

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DGIdb: mining the druggable genome von Griffith, Malachi, Griffith, Obi L, Coffman, Adam C, Weible, James V, McMichael, Josh F, Spies, Nicholas C, Koval, James, Das, Indraniel, Callaway, Matthew B, Eldred, James M, Miller, Christopher A, Subramanian, Janakiraman, Govindan, Ramaswamy, Kumar, Runjun D, Bose, Ron, Ding, Li, Walker, Jason R, Larson, David E, Dooling, David J, Smith, Scott M, Ley, Timothy J, Mardis, Elaine R, Wilson, Richard K

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