Search Results - "Meyerson, Matthew"

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

“…We describe methods with enhanced power and specificity to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By…”
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Advances in understanding cancer genomes through second-generation sequencing by Meyerson, Matthew, Gabriel, Stacey, Getz, Gad

“…Key Points Analyses of cancer genome sequences and structures provide insights for understanding cancer biology, diagnosis and therapy. The application of…”
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Targeted genomic rearrangements using CRISPR/Cas technology by Choi, Peter S., Meyerson, Matthew

“…Genomic rearrangements are frequently observed in cancer cells but have been difficult to generate in a highly specific manner for functional analysis. Here we…”
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Genomic insights into the mechanisms of FGFR1 dependency in squamous cell lung cancer by Mäkinen, Netta, Meyerson, Matthew

“…Although subsets of patients with lung squamous cell carcinoma (LSCC) benefit from immunotherapy, there are few effective molecularly targeted treatments for…”
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Chromothripsis from DNA damage in micronuclei by Zhang, Cheng-Zhong, Spektor, Alexander, Cornils, Hauke, Francis, Joshua M., Jackson, Emily K., Liu, Shiwei, Meyerson, Matthew, Pellman, David

“…Genome sequencing has uncovered a new mutational phenomenon in cancer and congenital disorders called chromothripsis. Chromothripsis is characterized by…”
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Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples by Cibulskis, Kristian, Lawrence, Michael S, Carter, Scott L, Sivachenko, Andrey, Jaffe, David, Sougnez, Carrie, Gabriel, Stacey, Meyerson, Matthew, Lander, Eric S, Getz, Gad

“…The MuTect algorithm for calling somatic point mutations enables subclonal analysis of the whole-genome or whole-exome sequencing data being generated in…”
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Patient-derived lung cancer organoids as in vitro cancer models for therapeutic screening by 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

“…Lung cancer shows substantial genetic and phenotypic heterogeneity across individuals, driving a need for personalised medicine. Here, we report lung cancer…”
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Whole-exome sequencing reveals frequent genetic alterations in BAP1, NF2, CDKN2A, and CUL1 in malignant pleural mesothelioma by Guo, Guangwu, Chmielecki, Juliann, Goparaju, Chandra, Heguy, Adriana, Dolgalev, Igor, Carbone, Michele, Seepo, Sara, Meyerson, Matthew, Pass, Harvey I

“…Malignant pleural mesothelioma (MPM) is an aggressive neoplasm associated with asbestos exposure. Although previous studies based on candidate gene approaches…”
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Genetic and transcriptional evolution alters cancer cell line drug response by 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.

“…Human cancer cell lines are the workhorse of cancer research. Although cell lines are known to evolve in culture, the extent of the resultant genetic and…”
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Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers by Zhang, Xiaoyang, Choi, Peter S, Francis, Joshua M, Imielinski, Marcin, Watanabe, Hideo, Cherniack, Andrew D, Meyerson, Matthew

“…Matthew Meyerson and colleagues identify focal amplifications of regions harboring super-enhancers near KLF5 , USP12 , PARD6B and MYC in epithelial cancers…”
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Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2 by Nomburg, Jason, Meyerson, Matthew, DeCaprio, James A

“…SARS-CoV-2, a positive-sense RNA virus in the family Coronaviridae, has caused a worldwide pandemic of coronavirus disease 2019 or COVID-19. Coronaviruses…”
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Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes by 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.

“…Diffuse large B cell lymphoma (DLBCL), the most common lymphoid malignancy in adults, is a clinically and genetically heterogeneous disease that is further…”
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Making sense of cancer genomic data by Chin, Lynda, Hahn, William C, Getz, Gad, Meyerson, Matthew

“…High-throughput tools for nucleic acid characterization now provide the means to conduct comprehensive analyses of all somatic alterations in the cancer…”
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Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas by 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

“…Matthew Meyerson, Ramaswamy Govindan and colleagues examine the exome sequences and copy number profiles of 660 lung adenocarcinoma and 484 lung squamous cell…”
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Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia by 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.

“…Mutations in SF3B1, which encodes a spliceosome component, are associated with poor outcome in chronic lymphocytic leukemia (CLL), but how these contribute to…”
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SvABA: genome-wide detection of structural variants and indels by local assembly by 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

“…Structural variants (SVs), including small insertion and deletion variants (indels), are challenging to detect through standard alignment-based variant calling…”
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Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing by Helman, Elena, Lawrence, Michael S, Stewart, Chip, Sougnez, Carrie, Getz, Gad, Meyerson, Matthew

“…Retrotransposons constitute a major source of genetic variation, and somatic retrotransposon insertions have been reported in cancer. Here, we applied…”
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Quantification of aneuploidy in targeted sequencing data using ASCETS by 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

“…Abstract Summary The expansion of targeted panel sequencing efforts has created opportunities for large-scale genomic analysis, but tools for copy-number…”
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Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing by Viswanathan, Srinivas R., Ha, Gavin, Hoff, Andreas M., Wala, Jeremiah A., Carrot-Zhang, Jian, Whelan, Christopher W., Haradhvala, Nicholas J., Freeman, Samuel S., Reed, Sarah C., Rhoades, Justin, Polak, Paz, Cipicchio, Michelle, Wankowicz, Stephanie A., Wong, Alicia, Kamath, Tushar, Zhang, Zhenwei, Gydush, Gregory J., Rotem, Denisse, Love, J. Christopher, Getz, Gad, Gabriel, Stacey, Zhang, Cheng-Zhong, Dehm, Scott M., Nelson, Peter S., Van Allen, Eliezer M., Choudhury, Atish D., Adalsteinsson, Viktor A., Beroukhim, Rameen, Taplin, Mary-Ellen, Meyerson, Matthew

“…Nearly all prostate cancer deaths are from metastatic castration-resistant prostate cancer (mCRPC), but there have been few whole-genome sequencing (WGS)…”
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Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres by Tan, Kar-Tong, Slevin, Michael K, Meyerson, Matthew, Li, Heng

“…Nanopore long-read sequencing is an emerging approach for studying genomes, including long repetitive elements like telomeres. Here, we report extensive…”
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