GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers von Mermel, Craig H, Schumacher, Steven E, Hill, Barbara, Meyerson, Matthew L, Beroukhim, Rameen, Getz, Gad

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Advances in understanding cancer genomes through second-generation sequencing von Meyerson, Matthew, Gabriel, Stacey, Getz, Gad

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Targeted genomic rearrangements using CRISPR/Cas technology von Choi, Peter S., Meyerson, Matthew

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Genomic insights into the mechanisms of FGFR1 dependency in squamous cell lung cancer von Mäkinen, Netta, Meyerson, Matthew

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Chromothripsis from DNA damage in micronuclei von Zhang, Cheng-Zhong, Spektor, Alexander, Cornils, Hauke, Francis, Joshua M., Jackson, Emily K., Liu, Shiwei, Meyerson, Matthew, Pellman, David

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Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples von Cibulskis, Kristian, Lawrence, Michael S, Carter, Scott L, Sivachenko, Andrey, Jaffe, David, Sougnez, Carrie, Gabriel, Stacey, Meyerson, Matthew, Lander, Eric S, Getz, Gad

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Patient-derived lung cancer organoids as in vitro cancer models for therapeutic screening von Kim, Minsuh, Mun, Hyemin, Sung, Chang Oak, Cho, Eun Jeong, Jeon, Hye-Joon, Chun, Sung-Min, Jung, Da Jung, Shin, Tae Hoon, Jeong, Gi Seok, Kim, Dong Kwan, Choi, Eun Kyung, Jeong, Seong-Yun, Taylor, Alison M., Jain, Sejal, Meyerson, Matthew, Jang, Se Jin

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Whole-exome sequencing reveals frequent genetic alterations in BAP1, NF2, CDKN2A, and CUL1 in malignant pleural mesothelioma von Guo, Guangwu, Chmielecki, Juliann, Goparaju, Chandra, Heguy, Adriana, Dolgalev, Igor, Carbone, Michele, Seepo, Sara, Meyerson, Matthew, Pass, Harvey I

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Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes von Chapuy, Bjoern, Stewart, Chip, Dunford, Andrew J., Kim, Jaegil, Kamburov, Atanas, Redd, Robert A., Lawrence, Mike S., Roemer, Margaretha G. M., Li, Amy J., Ziepert, Marita, Staiger, Annette M., Wala, Jeremiah A., Ducar, Matthew D., Leshchiner, Ignaty, Rheinbay, Ester, Taylor-Weiner, Amaro, Coughlin, Caroline A., Hess, Julian M., Pedamallu, Chandra S., Livitz, Dimitri, Rosebrock, Daniel, Rosenberg, Mara, Tracy, Adam A., Horn, Heike, van Hummelen, Paul, Feldman, Andrew L., Link, Brian K., Novak, Anne J., Cerhan, James R., Habermann, Thomas M., Siebert, Reiner, Rosenwald, Andreas, Thorner, Aaron R., Meyerson, Matthew L., Golub, Todd R., Beroukhim, Rameen, Wulf, Gerald G., Ott, German, Rodig, Scott J., Monti, Stefano, Neuberg, Donna S., Loeffler, Markus, Pfreundschuh, Michael, Trümper, Lorenz, Getz, Gad, Shipp, Margaret A.

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Genetic and transcriptional evolution alters cancer cell line drug response von Ben-David, Uri, Siranosian, Benjamin, Ha, Gavin, Tang, Helen, Oren, Yaara, Hinohara, Kunihiko, Strathdee, Craig A., Dempster, Joshua, Lyons, Nicholas J., Burns, Robert, Nag, Anwesha, Kugener, Guillaume, Cimini, Beth, Tsvetkov, Peter, Maruvka, Yosef E., O’Rourke, Ryan, Garrity, Anthony, Tubelli, Andrew A., Bandopadhayay, Pratiti, Tsherniak, Aviad, Vazquez, Francisca, Wong, Bang, Birger, Chet, Ghandi, Mahmoud, Thorner, Aaron R., Bittker, Joshua A., Meyerson, Matthew, Getz, Gad, Beroukhim, Rameen, Golub, Todd R.

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Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers von Zhang, Xiaoyang, Choi, Peter S, Francis, Joshua M, Imielinski, Marcin, Watanabe, Hideo, Cherniack, Andrew D, Meyerson, Matthew

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Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia von Wang, Lili, Brooks, Angela N., Fan, Jean, Wan, Youzhong, Gambe, Rutendo, Li, Shuqiang, Hergert, Sarah, Yin, Shanye, Freeman, Samuel S., Levin, Joshua Z., Fan, Lin, Seiler, Michael, Buonamici, Silvia, Smith, Peter G., Chau, Kevin F., Cibulskis, Carrie L., Zhang, Wandi, Rassenti, Laura Z., Ghia, Emanuela M., Kipps, Thomas J., Fernandes, Stacey, Bloch, Donald B., Kotliar, Dylan, Landau, Dan A., Shukla, Sachet A., Aster, Jon C., Reed, Robin, DeLuca, David S., Brown, Jennifer R., Neuberg, Donna, Getz, Gad, Livak, Kenneth J., Meyerson, Matthew M., Kharchenko, Peter V., Wu, Catherine J.

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Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2 von Nomburg, Jason, Meyerson, Matthew, DeCaprio, James A

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Dissecting Therapeutic Resistance to RAF Inhibition in Melanoma by Tumor Genomic Profiling von WAGLE, Nikhil, EMERY, Caroline, MEYERSON, Matthew, GARRAWAY, Levi A, BERGER, Michael F, DAVIS, Matthew J, SAWYER, Allison, POCHANARD, Panisa, KEHOE, Sarah M, JOHANNESSEN, Cory M, MACCONAILL, Laura E, HAHN, William C

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Making sense of cancer genomic data von Chin, Lynda, Hahn, William C, Getz, Gad, Meyerson, Matthew

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Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing von MacConaill, Laura E, Burns, Robert T, Nag, Anwesha, Coleman, Haley A, Slevin, Michael K, Giorda, Kristina, Light, Madelyn, Lai, Kevin, Jarosz, Mirna, McNeill, Matthew S, Ducar, Matthew D, Meyerson, Matthew, Thorner, Aaron R

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Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas von Campbell, Joshua D, Alexandrov, Anton, Kim, Jaegil, Wala, Jeremiah, Berger, Alice H, Pedamallu, Chandra Sekhar, Shukla, Sachet A, Guo, Guangwu, Brooks, Angela N, Murray, Bradley A, Imielinski, Marcin, Hu, Xin, Ling, Shiyun, Akbani, Rehan, Rosenberg, Mara, Cibulskis, Carrie, Ramachandran, Aruna, Collisson, Eric A, Kwiatkowski, David J, Lawrence, Michael S, Weinstein, John N, Verhaak, Roel G W, Wu, Catherine J, Hammerman, Peter S, Cherniack, Andrew D, Getz, Gad, Artyomov, Maxim N, Schreiber, Robert, Govindan, Ramaswamy, Meyerson, Matthew

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SvABA: genome-wide detection of structural variants and indels by local assembly von Wala, Jeremiah A, Bandopadhayay, Pratiti, Greenwald, Noah F, O'Rourke, Ryan, Sharpe, Ted, Stewart, Chip, Schumacher, Steve, Li, Yilong, Weischenfeldt, Joachim, Yao, Xiaotong, Nusbaum, Chad, Campbell, Peter, Getz, Gad, Meyerson, Matthew, Zhang, Cheng-Zhong, Imielinski, Marcin, Beroukhim, Rameen

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Quantification of aneuploidy in targeted sequencing data using ASCETS von Spurr, Liam F, Touat, Mehdi, Taylor, Alison M, Dubuc, Adrian M, Shih, Juliann, Meredith, David M, Pisano, William V, Meyerson, Matthew L, Ligon, Keith L, Cherniack, Andrew D, Li, Yvonne Y, Beroukhim, Rameen

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Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres von Tan, Kar-Tong, Slevin, Michael K, Meyerson, Matthew, Li, Heng

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