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318 results on '"Winckler, Wendy"'

1. Supplementary Table S3 from Sensitive MRD Detection from Lymphatic Fluid after Surgery in HPV-Associated Oropharyngeal Cancer

Author

Earland, Noah, primary, Semenkovich, Nicholas P., primary, Ramirez, Ricardo J., primary, Gerndt, Sophie P., primary, Harris, Peter K., primary, Gu, Zhuosheng, primary, Hearn, Andrew I., primary, Inkman, Matthew, primary, Szymanski, Jeffrey J., primary, Whitfield, Damion, primary, Wahle, Benjamin M., primary, Xu, Zhongping, primary, Chen, Kevin, primary, Alahi, Irfan, primary, Ni, Gabris, primary, Chen, Andrew, primary, Winckler, Wendy, primary, Zhang, Jin, primary, Chaudhuri, Aadel A., primary, and Zevallos, Jose P., primary

Published
2024
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2. Data from Sensitive MRD Detection from Lymphatic Fluid after Surgery in HPV-Associated Oropharyngeal Cancer

Author

Earland, Noah, primary, Semenkovich, Nicholas P., primary, Ramirez, Ricardo J., primary, Gerndt, Sophie P., primary, Harris, Peter K., primary, Gu, Zhuosheng, primary, Hearn, Andrew I., primary, Inkman, Matthew, primary, Szymanski, Jeffrey J., primary, Whitfield, Damion, primary, Wahle, Benjamin M., primary, Xu, Zhongping, primary, Chen, Kevin, primary, Alahi, Irfan, primary, Ni, Gabris, primary, Chen, Andrew, primary, Winckler, Wendy, primary, Zhang, Jin, primary, Chaudhuri, Aadel A., primary, and Zevallos, Jose P., primary

Published
2024
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3. Supplementary Figure S5 from Sensitive MRD Detection from Lymphatic Fluid after Surgery in HPV-Associated Oropharyngeal Cancer

Author

Earland, Noah, primary, Semenkovich, Nicholas P., primary, Ramirez, Ricardo J., primary, Gerndt, Sophie P., primary, Harris, Peter K., primary, Gu, Zhuosheng, primary, Hearn, Andrew I., primary, Inkman, Matthew, primary, Szymanski, Jeffrey J., primary, Whitfield, Damion, primary, Wahle, Benjamin M., primary, Xu, Zhongping, primary, Chen, Kevin, primary, Alahi, Irfan, primary, Ni, Gabris, primary, Chen, Andrew, primary, Winckler, Wendy, primary, Zhang, Jin, primary, Chaudhuri, Aadel A., primary, and Zevallos, Jose P., primary

Published
2024
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4. Supplementary Methods S1 from Sensitive MRD Detection from Lymphatic Fluid after Surgery in HPV-Associated Oropharyngeal Cancer

Author

Earland, Noah, primary, Semenkovich, Nicholas P., primary, Ramirez, Ricardo J., primary, Gerndt, Sophie P., primary, Harris, Peter K., primary, Gu, Zhuosheng, primary, Hearn, Andrew I., primary, Inkman, Matthew, primary, Szymanski, Jeffrey J., primary, Whitfield, Damion, primary, Wahle, Benjamin M., primary, Xu, Zhongping, primary, Chen, Kevin, primary, Alahi, Irfan, primary, Ni, Gabris, primary, Chen, Andrew, primary, Winckler, Wendy, primary, Zhang, Jin, primary, Chaudhuri, Aadel A., primary, and Zevallos, Jose P., primary

Published
2024
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5. High-throughput identification of genotype-specific cancer vulnerabilities in mixtures of barcoded tumor cell lines

Author

Yu, Channing, Mannan, Aristotle M, Yvone, Griselda Metta, Ross, Kenneth N, Zhang, Yan-Ling, Marton, Melissa A, Taylor, Bradley R, Crenshaw, Andrew, Gould, Joshua Z, Tamayo, Pablo, Weir, Barbara A, Tsherniak, Aviad, Wong, Bang, Garraway, Levi A, Shamji, Alykhan F, Palmer, Michelle A, Foley, Michael A, Winckler, Wendy, Schreiber, Stuart L, Kung, Andrew L, and Golub, Todd R

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Cancer, Animals, Cell Line, Tumor, DNA Barcoding, Taxonomic, Drug Resistance, Neoplasm, Genotyping Techniques, High-Throughput Nucleotide Sequencing, Humans, Mice, Neoplasms
Abstract

Hundreds of genetically characterized cell lines are available for the discovery of genotype-specific cancer vulnerabilities. However, screening large numbers of compounds against large numbers of cell lines is currently impractical, and such experiments are often difficult to control. Here we report a method called PRISM that allows pooled screening of mixtures of cancer cell lines by labeling each cell line with 24-nucleotide barcodes. PRISM revealed the expected patterns of cell killing seen in conventional (unpooled) assays. In a screen of 102 cell lines across 8,400 compounds, PRISM led to the identification of BRD-7880 as a potent and highly specific inhibitor of aurora kinases B and C. Cell line pools also efficiently formed tumors as xenografts, and PRISM recapitulated the expected pattern of erlotinib sensitivity in vivo.

Published
2016

6. Cell-free DNA captures tumor heterogeneity and driver alterations in rapid autopsies with pre-treated metastatic cancer

Author

Pereira, Bernard, Chen, Christopher T., Goyal, Lipika, Walmsley, Charlotte, Pinto, Christopher J., Baiev, Islam, Allen, Read, Henderson, Laura, Saha, Supriya, Reyes, Stephanie, Taylor, Martin S., Fitzgerald, Donna M., Broudo, Maida Williams, Sahu, Avinash, Gao, Xin, Winckler, Wendy, Brannon, A. Rose, Engelman, Jeffrey A., Leary, Rebecca, Stone, James R., Campbell, Catarina D., and Juric, Dejan

Published
2021
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7. Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico

Author

Williams, Amy L, Jacobs, Suzanne BR, Moreno-Macías, Hortensia, Huerta-Chagoya, Alicia, Churchhouse, Claire, Márquez-Luna, Carla, García-Ortíz, Humberto, José Gómez-Vázquez, María, Burtt, Noël P, Aguilar-Salinas, Carlos A, González-Villalpando, Clicerio, Florez, Jose C, Orozco, Lorena, Haiman, Christopher A, Tusié-Luna, Teresa, Altshuler, David, Ripke, Stephan, Manning, Alisa K, Neale, Benjamin, Reich, David, Stram, Daniel O, Fernández-López, Juan Carlos, Romero-Hidalgo, Sandra, Patterson, Nick, Aguilar-Delfín, Irma, Martínez-Hernández, Angélica, Centeno-Cruz, Federico, Mendoza-Caamal, Elvia, Revilla-Monsalve, Cristina, Islas-Andrade, Sergio, Córdova, Emilio, Rodríguez-Arellano, Eunice, Soberón, Xavier, González-Villalpando, María Elena, Henderson, Brian E, Monroe, Kristine, Wilkens, Lynne, Kolonel, Laurence N, Le Marchand, Loic, Riba, Laura, Ordóñez-Sánchez, María Luisa, Rodríguez-Guillén, Rosario, Cruz-Bautista, Ivette, Rodríguez-Torres, Maribel, Muñoz-Hernández, Linda Liliana, Sáenz, Tamara, Gómez, Donají, Alvirde, Ulices, Onofrio, Robert C, Brodeur, Wendy M, Gage, Diane, Murphy, Jacquelyn, Franklin, Jennifer, Mahan, Scott, Ardlie, Kristin, Crenshaw, Andrew T, Winckler, Wendy, Prüfer, Kay, Shunkov, Michael V, Sawyer, Susanna, Stenzel, Udo, Kelso, Janet, Lek, Monkol, Sankararaman, Sriram, MacArthur, Daniel G, Derevianko, Anatoli P, Pääbo, Svante, Gopal, Shuba, Grammatikos, James A, Smith, Ian C, Bullock, Kevin H, Deik, Amy A, Souza, Amanda L, Pierce, Kerry A, Clish, Clary B, Fennell, Timothy, and Farjoun, Yossi

Subjects
Nutrition, Diabetes, Prevention, Genetics, 2.1 Biological and endogenous factors, Aetiology, Metabolic and endocrine, Alleles, Animals, Asian People, Black People, Cohort Studies, Diabetes Mellitus, Type 2, Endoplasmic Reticulum, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Haplotypes, HeLa Cells, Humans, Indians, North American, Lipid Metabolism, Liver, Male, Mexico, Monocarboxylic Acid Transporters, Neanderthals, Polymorphism, Single Nucleotide, RNA, Messenger, Triglycerides, White People, SIGMA Type 2 Diabetes Consortium, Hela Cells, General Science & Technology
Abstract

Performing genetic studies in multiple human populations can identify disease risk alleles that are common in one population but rare in others, with the potential to illuminate pathophysiology, health disparities, and the population genetic origins of disease alleles. Here we analysed 9.2 million single nucleotide polymorphisms (SNPs) in each of 8,214 Mexicans and other Latin Americans: 3,848 with type 2 diabetes and 4,366 non-diabetic controls. In addition to replicating previous findings, we identified a novel locus associated with type 2 diabetes at genome-wide significance spanning the solute carriers SLC16A11 and SLC16A13 (P = 3.9 × 10(-13); odds ratio (OR) = 1.29). The association was stronger in younger, leaner people with type 2 diabetes, and replicated in independent samples (P = 1.1 × 10(-4); OR = 1.20). The risk haplotype carries four amino acid substitutions, all in SLC16A11; it is present at ~50% frequency in Native American samples and ~10% in east Asian, but is rare in European and African samples. Analysis of an archaic genome sequence indicated that the risk haplotype introgressed into modern humans via admixture with Neanderthals. The SLC16A11 messenger RNA is expressed in liver, and V5-tagged SLC16A11 protein localizes to the endoplasmic reticulum. Expression of SLC16A11 in heterologous cells alters lipid metabolism, most notably causing an increase in intracellular triacylglycerol levels. Despite type 2 diabetes having been well studied by genome-wide association studies in other populations, analysis in Mexican and Latin American individuals identified SLC16A11 as a novel candidate gene for type 2 diabetes with a possible role in triacylglycerol metabolism.

Published
2014

8. Sensitive MRD Detection from Lymphatic Fluid after Surgery in HPV-Associated Oropharyngeal Cancer

Author

Earland, Noah, primary, Semenkovich, Nicholas P., additional, Ramirez, Ricardo J., additional, Gerndt, Sophie P., additional, Harris, Peter K., additional, Gu, Zhuosheng, additional, Hearn, Andrew I., additional, Inkman, Matthew, additional, Szymanski, Jeffrey J., additional, Whitfield, Damion, additional, Wahle, Benjamin M., additional, Xu, Zhongping, additional, Chen, Kevin, additional, Alahi, Irfan, additional, Ni, Gabris, additional, Chen, Andrew, additional, Winckler, Wendy, additional, Zhang, Jin, additional, Chaudhuri, Aadel A., additional, and Zevallos, Jose P., additional

Published
2023
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9. Abstract PR09: Detection of minimal residual disease in post-surgical drain fluid can predict locoregional recurrence in HPV-negative head and neck cancer patients

Author

Chaudhuri, Aadel A., primary, Gu, Zhuosheng, additional, Whitfield, Damion, additional, Earland, Noah, additional, Harmon, Adam, additional, Long, Megan, additional, Harris, Peter, additional, Xu, Zhongping, additional, Ramirez, Ricardo, additional, Gerndt, Sophie, additional, Pacula, Maciej, additional, Francis, Marra S., additional, Winckler, Wendy, additional, and Zevallos, Jose P., additional

Published
2023
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10. Integrated genomic characterization of endometrial carcinoma

Author

Getz, Gad, Gabriel, Stacey B, Cibulskis, Kristian, Lander, Eric, Sivachenko, Andrey, Sougnez, Carrie, Lawrence, Mike, Kandoth, Cyriac, Dooling, David, Fulton, Robert, Fulton, Lucinda, Kalicki-Veizer, Joelle, McLellan, Michael D, O’Laughlin, Michelle, Schmidt, Heather, Wilson, Richard K, Ye, Kai, Ding, Li, Mardis, Elaine R, Ally, Adrian, Balasundaram, Miruna, Birol, Inanc, Butterfield, Yaron SN, Carlsen, Rebecca, Carter, Candace, Chu, Andy, Chuah, Eric, Chun, Hye-Jung E, Dhalla, Noreen, Guin, Ranabir, Hirst, Carrie, Holt, Robert A, Jones, Steven JM, Lee, Darlene, Li, Haiyan I, Marra, Marco A, Mayo, Michael, Moore, Richard A, Mungall, Andrew J, Plettner, Patrick, Schein, Jacqueline E, Sipahimalani, Payal, Tam, Angela, Varhol, Richard J, Gordon Robertson, A, Cherniack, Andrew D, Pashtan, Itai, Saksena, Gordon, Onofrio, Robert C, Schumacher, Steven E, Tabak, Barbara, Carter, Scott L, Hernandez, Bryan, Gentry, Jeff, Salvesen, Helga B, Ardlie, Kristin, Winckler, Wendy, Beroukhim, Rameen, Meyerson, Matthew, Hadjipanayis, Angela, Lee, Semin, Mahadeshwar, Harshad S, Park, Peter, Protopopov, Alexei, Ren, Xiaojia, Seth, Sahil, Song, Xingzhi, Tang, Jiabin, Xi, Ruibin, Yang, Lixing, Zeng, Dong, Kucherlapati, Raju, Chin, Lynda, Zhang, Jianhua, Todd Auman, J, Balu, Saianand, Bodenheimer, Tom, Buda, Elizabeth, Neil Hayes, D, Hoyle, Alan P, Jefferys, Stuart R, Jones, Corbin D, Meng, Shaowu, Mieczkowski, Piotr A, Mose, Lisle E, Parker, Joel S, Perou, Charles M, Roach, Jeff, Shi, Yan, Simons, Janae V, Soloway, Mathew G, Tan, Donghui, Topal, Michael D, Waring, Scot, Wu, Junyuan, Hoadley, Katherine A, Baylin, Stephen B, and Bootwalla, Moiz S

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Oncology and Carcinogenesis, Reproductive Medicine, Human Genome, Cancer, Uterine Cancer, Biotechnology, Breast Neoplasms, Chromosome Aberrations, DNA Copy Number Variations, DNA Mutational Analysis, DNA Polymerase II, DNA-Binding Proteins, Endometrial Neoplasms, Exome, Female, Gene Expression Regulation, Neoplastic, Genome, Human, Genomics, Humans, Ovarian Neoplasms, Poly-ADP-Ribose Binding Proteins, Signal Transduction, Transcription Factors, Cancer Genome Atlas Research Network, General Science & Technology
Abstract

We performed an integrated genomic, transcriptomic and proteomic characterization of 373 endometrial carcinomas using array- and sequencing-based technologies. Uterine serous tumours and ∼25% of high-grade endometrioid tumours had extensive copy number alterations, few DNA methylation changes, low oestrogen receptor/progesterone receptor levels, and frequent TP53 mutations. Most endometrioid tumours had few copy number alterations or TP53 mutations, but frequent mutations in PTEN, CTNNB1, PIK3CA, ARID1A and KRAS and novel mutations in the SWI/SNF chromatin remodelling complex gene ARID5B. A subset of endometrioid tumours that we identified had a markedly increased transversion mutation frequency and newly identified hotspot mutations in POLE. Our results classified endometrial cancers into four categories: POLE ultramutated, microsatellite instability hypermutated, copy-number low, and copy-number high. Uterine serous carcinomas share genomic features with ovarian serous and basal-like breast carcinomas. We demonstrated that the genomic features of endometrial carcinomas permit a reclassification that may affect post-surgical adjuvant treatment for women with aggressive tumours.

Published
2013

11. Comprehensive genomic characterization of squamous cell lung cancers

Author

Hammerman, Peter S, Lawrence, Michael S, Voet, Douglas, Jing, Rui, Cibulskis, Kristian, Sivachenko, Andrey, Stojanov, Petar, McKenna, Aaron, Lander, Eric S, Gabriel, Stacey, Getz, Gad, Sougnez, Carrie, Imielinski, Marcin, Helman, Elena, Hernandez, Bryan, Pho, Nam H, Meyerson, Matthew, Chu, Andy, Chun, Hye-Jung E, Mungall, Andrew J, Pleasance, Erin, Gordon Robertson, A, Sipahimalani, Payal, Stoll, Dominik, Balasundaram, Miruna, Birol, Inanc, Butterfield, Yaron SN, Chuah, Eric, Coope, Robin JN, Corbett, Richard, Dhalla, Noreen, Guin, Ranabir, He, An, Hirst, Carrie, Hirst, Martin, Holt, Robert A, Lee, Darlene, Li, Haiyan I, Mayo, Michael, Moore, Richard A, Mungall, Karen, Ming Nip, Ka, Olshen, Adam, Schein, Jacqueline E, Slobodan, Jared R, Tam, Angela, Thiessen, Nina, Varhol, Richard, Zeng, Thomas, Zhao, Yongjun, Jones, Steven JM, Marra, Marco A, Saksena, Gordon, Cherniack, Andrew D, Schumacher, Stephen E, Tabak, Barbara, Carter, Scott L, Nguyen, Huy, Onofrio, Robert C, Crenshaw, Andrew, Ardlie, Kristin, Beroukhim, Rameen, Winckler, Wendy, Protopopov, Alexei, Zhang, Jianhua, Hadjipanayis, Angela, Lee, Semin, Xi, Ruibin, Yang, Lixing, Ren, Xiaojia, Zhang, Hailei, Shukla, Sachet, Chen, Peng-Chieh, Haseley, Psalm, Lee, Eunjung, Chin, Lynda, Park, Peter J, Kucherlapati, Raju, Socci, Nicholas D, Liang, Yupu, Schultz, Nikolaus, Borsu, Laetitia, Lash, Alex E, Viale, Agnes, Sander, Chris, Ladanyi, Marc, Todd Auman, J, Hoadley, Katherine A, Wilkerson, Matthew D, Shi, Yan, Liquori, Christina, Meng, Shaowu, Li, Ling, Turman, Yidi J, Topal, Michael D, and Tan, Donghui

Subjects
Human Genome, Biotechnology, Genetics, Rare Diseases, Cancer, Lung Cancer, Lung, Aetiology, 2.1 Biological and endogenous factors, Adenocarcinoma, Adenocarcinoma of Lung, Carcinoma, Squamous Cell, DNA Mutational Analysis, Gene Deletion, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Genes, p16, Genes, p53, Genome, Human, Genomics, Humans, Lung Neoplasms, Molecular Targeted Therapy, Mutation, Mutation Rate, Phosphatidylinositol 3-Kinases, Signal Transduction, Cancer Genome Atlas Research Network, General Science & Technology
Abstract

Lung squamous cell carcinoma is a common type of lung cancer, causing approximately 400,000 deaths per year worldwide. Genomic alterations in squamous cell lung cancers have not been comprehensively characterized, and no molecularly targeted agents have been specifically developed for its treatment. As part of The Cancer Genome Atlas, here we profile 178 lung squamous cell carcinomas to provide a comprehensive landscape of genomic and epigenomic alterations. We show that the tumour type is characterized by complex genomic alterations, with a mean of 360 exonic mutations, 165 genomic rearrangements, and 323 segments of copy number alteration per tumour. We find statistically recurrent mutations in 11 genes, including mutation of TP53 in nearly all specimens. Previously unreported loss-of-function mutations are seen in the HLA-A class I major histocompatibility gene. Significantly altered pathways included NFE2L2 and KEAP1 in 34%, squamous differentiation genes in 44%, phosphatidylinositol-3-OH kinase pathway genes in 47%, and CDKN2A and RB1 in 72% of tumours. We identified a potential therapeutic target in most tumours, offering new avenues of investigation for the treatment of squamous cell lung cancers.

Published
2012

13. Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy

Author

Barretina, Jordi, Taylor, Barry S, Banerji, Shantanu, Ramos, Alexis H, Lagos-Quintana, Mariana, DeCarolis, Penelope L, Shah, Kinjal, Socci, Nicholas D, Weir, Barbara A, Ho, Alan, Chiang, Derek Y, Reva, Boris, Mermel, Craig H, Getz, Gad, Antipin, Yevgenyi, Beroukhim, Rameen, Major, John E, Hatton, Charles, Nicoletti, Richard, Hanna, Megan, Sharpe, Ted, Fennell, Tim J, Cibulskis, Kristian, Onofrio, Robert C, Saito, Tsuyoshi, Shukla, Neerav, Lau, Christopher, Nelander, Sven, Silver, Serena J, Sougnez, Carrie, Viale, Agnes, Winckler, Wendy, Maki, Robert G, Garraway, Levi A, Lash, Alex, Greulich, Heidi, Root, David E, Sellers, William R, Schwartz, Gary K, Antonescu, Cristina R, Lander, Eric S, Varmus, Harold E, Ladanyi, Marc, Sander, Chris, Meyerson, Matthew, and Singer, Samuel

Subjects
Pediatric, Biotechnology, Cancer, Human Genome, Genetics, Adult, Aged, Female, Genes, Tumor Suppressor, Genome, Histiocytoma, Malignant Fibrous, Humans, Liposarcoma, Male, Middle Aged, Mutation, Sarcoma, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Soft-tissue sarcomas, which result in approximately 10,700 diagnoses and 3,800 deaths per year in the United States, show remarkable histologic diversity, with more than 50 recognized subtypes. However, knowledge of their genomic alterations is limited. We describe an integrative analysis of DNA sequence, copy number and mRNA expression in 207 samples encompassing seven major subtypes. Frequently mutated genes included TP53 (17% of pleomorphic liposarcomas), NF1 (10.5% of myxofibrosarcomas and 8% of pleomorphic liposarcomas) and PIK3CA (18% of myxoid/round-cell liposarcomas, or MRCs). PIK3CA mutations in MRCs were associated with Akt activation and poor clinical outcomes. In myxofibrosarcomas and pleomorphic liposarcomas, we found both point mutations and genomic deletions affecting the tumor suppressor NF1. Finally, we found that short hairpin RNA (shRNA)-based knockdown of several genes amplified in dedifferentiated liposarcoma, including CDK4 and YEATS4, decreased cell proliferation. Our study yields a detailed map of molecular alterations across diverse sarcoma subtypes and suggests potential subtype-specific targets for therapy.

Published
2010

14. Comprehensive genomic characterization defines human glioblastoma genes and core pathways

Author

McLendon, Roger, Friedman, Allan, Bigner, Darrell, Van Meir, Erwin G, Brat, Daniel J, M. Mastrogianakis, Gena, Olson, Jeffrey J, Mikkelsen, Tom, Lehman, Norman, Aldape, Ken, Alfred Yung, WK, Bogler, Oliver, VandenBerg, Scott, Berger, Mitchel, Prados, Michael, Muzny, Donna, Morgan, Margaret, Scherer, Steve, Sabo, Aniko, Nazareth, Lynn, Lewis, Lora, Hall, Otis, Zhu, Yiming, Ren, Yanru, Alvi, Omar, Yao, Jiqiang, Hawes, Alicia, Jhangiani, Shalini, Fowler, Gerald, San Lucas, Anthony, Kovar, Christie, Cree, Andrew, Dinh, Huyen, Santibanez, Jireh, Joshi, Vandita, Gonzalez-Garay, Manuel L, Miller, Christopher A, Milosavljevic, Aleksandar, Donehower, Larry, Wheeler, David A, Gibbs, Richard A, Cibulskis, Kristian, Sougnez, Carrie, Fennell, Tim, Mahan, Scott, Wilkinson, Jane, Ziaugra, Liuda, Onofrio, Robert, Bloom, Toby, Nicol, Rob, Ardlie, Kristin, Baldwin, Jennifer, Gabriel, Stacey, Lander, Eric S, Ding, Li, Fulton, Robert S, McLellan, Michael D, Wallis, John, Larson, David E, Shi, Xiaoqi, Abbott, Rachel, Fulton, Lucinda, Chen, Ken, Koboldt, Daniel C, Wendl, Michael C, Meyer, Rick, Tang, Yuzhu, Lin, Ling, Osborne, John R, Dunford-Shore, Brian H, Miner, Tracie L, Delehaunty, Kim, Markovic, Chris, Swift, Gary, Courtney, William, Pohl, Craig, Abbott, Scott, Hawkins, Amy, Leong, Shin, Haipek, Carrie, Schmidt, Heather, Wiechert, Maddy, Vickery, Tammi, Scott, Sacha, Dooling, David J, Chinwalla, Asif, Weinstock, George M, Mardis, Elaine R, Wilson, Richard K, Getz, Gad, Winckler, Wendy, Verhaak, Roel GW, Lawrence, Michael S, O’Kelly, Michael, Robinson, Jim, Alexe, Gabriele, Beroukhim, Rameen, Carter, Scott, Chiang, Derek, and Gould, Josh

Subjects
Cancer, Human Genome, Genetic Testing, Brain Cancer, Genetics, Brain Disorders, Biotechnology, Rare Diseases, Aetiology, 2.1 Biological and endogenous factors, Adolescent, Adult, Aged, Aged, 80 and over, Brain Neoplasms, DNA Methylation, DNA Modification Methylases, DNA Repair, DNA Repair Enzymes, Female, Gene Dosage, Gene Expression Regulation, Neoplastic, Genes, Tumor Suppressor, Genes, erbB-1, Genome, Human, Genomics, Glioblastoma, Humans, Male, Middle Aged, Models, Molecular, Mutation, Neurofibromin 1, Phosphatidylinositol 3-Kinases, Protein Structure, Tertiary, Retrospective Studies, Signal Transduction, Tumor Suppressor Proteins, Cancer Genome Atlas Research Network, General Science & Technology
Abstract

Human cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation. The Cancer Genome Atlas (TCGA) pilot project aims to assess the value of large-scale multi-dimensional analysis of these molecular characteristics in human cancer and to provide the data rapidly to the research community. Here we report the interim integrative analysis of DNA copy number, gene expression and DNA methylation aberrations in 206 glioblastomas--the most common type of adult brain cancer--and nucleotide sequence aberrations in 91 of the 206 glioblastomas. This analysis provides new insights into the roles of ERBB2, NF1 and TP53, uncovers frequent mutations of the phosphatidylinositol-3-OH kinase regulatory subunit gene PIK3R1, and provides a network view of the pathways altered in the development of glioblastoma. Furthermore, integration of mutation, DNA methylation and clinical treatment data reveals a link between MGMT promoter methylation and a hypermutator phenotype consequent to mismatch repair deficiency in treated glioblastomas, an observation with potential clinical implications. Together, these findings establish the feasibility and power of TCGA, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer.

Published
2008

15. Author Correction: Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features

Author

Pitt, Jason J., Riester, Markus, Zheng, Yonglan, Yoshimatsu, Toshio F., Sanni, Ayodele, Oluwasola, Olayiwola, Veloso, Artur, Labrot, Emma, Wang, Shengfeng, Odetunde, Abayomi, Ademola, Adeyinka, Okedere, Babajide, Mahan, Scott, Leary, Rebecca, Macomber, Maura, Ajani, Mustapha, Johnson, Ryan S., Fitzgerald, Dominic, Grundstad, A. Jason, Tuteja, Jigyasa H., Khramtsova, Galina, Zhang, Jing, Sveen, Elisabeth, Hwang, Bryce, Clayton, Wendy, Nkwodimmah, Chibuzor, Famooto, Bisola, Obasi, Esther, Aderoju, Victor, Oludara, Mobolaji, Omodele, Folusho, Akinyele, Odunayo, Adeoye, Adewunmi, Ogundiran, Temidayo, Babalola, Chinedum, MacIsaac, Kenzie, Popoola, Abiodun, Morrissey, Michael P., Chen, Lin S., Wang, Jiebiao, Olopade, Christopher O., Falusi, Adeyinka G., Winckler, Wendy, Haase, Kerstin, Van Loo, Peter, Obafunwa, John, Papoutsakis, Dimitris, Ojengbede, Oladosu, Weber, Barbara, Ibrahim, Nasiru, White, Kevin P., Huo, Dezheng, Olopade, Olufunmilayo I., and Barretina, Jordi

Published
2019
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16. Data from Mutations in the DDR2 Kinase Gene Identify a Novel Therapeutic Target in Squamous Cell Lung Cancer

Author

Hammerman, Peter S., primary, Sos, Martin L., primary, Ramos, Alex H., primary, Xu, Chunxiao, primary, Dutt, Amit, primary, Zhou, Wenjun, primary, Brace, Lear E., primary, Woods, Brittany A., primary, Lin, Wenchu, primary, Zhang, Jianming, primary, Deng, Xianming, primary, Lim, Sang Min, primary, Heynck, Stefanie, primary, Peifer, Martin, primary, Simard, Jeffrey R., primary, Lawrence, Michael S., primary, Onofrio, Robert C., primary, Salvesen, Helga B., primary, Seidel, Danila, primary, Zander, Thomas, primary, Heuckmann, Johannes M., primary, Soltermann, Alex, primary, Moch, Holger, primary, Koker, Mirjam, primary, Leenders, Frauke, primary, Gabler, Franziska, primary, Querings, Silvia, primary, Ansén, Sascha, primary, Brambilla, Elisabeth, primary, Brambilla, Christian, primary, Lorimier, Philippe, primary, Brustugun, Odd Terje, primary, Helland, Åslaug, primary, Petersen, Iver, primary, Clement, Joachim H., primary, Groen, Harry, primary, Timens, Wim, primary, Sietsma, Hannie, primary, Stoelben, Erich, primary, Wolf, Jürgen, primary, Beer, David G., primary, Tsao, Ming Sound, primary, Hanna, Megan, primary, Hatton, Charles, primary, Eck, Michael J., primary, Janne, Pasi A., primary, Johnson, Bruce E., primary, Winckler, Wendy, primary, Greulich, Heidi, primary, Bass, Adam J., primary, Cho, Jeonghee, primary, Rauh, Daniel, primary, Gray, Nathanael S., primary, Wong, Kwok-Kin, primary, Haura, Eric B., primary, Thomas, Roman K., primary, and Meyerson, Matthew, primary

Published
2023
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17. Interview with Dr. Meyerson from Mutations in the DDR2 Kinase Gene Identify a Novel Therapeutic Target in Squamous Cell Lung Cancer

Author

Hammerman, Peter S., primary, Sos, Martin L., primary, Ramos, Alex H., primary, Xu, Chunxiao, primary, Dutt, Amit, primary, Zhou, Wenjun, primary, Brace, Lear E., primary, Woods, Brittany A., primary, Lin, Wenchu, primary, Zhang, Jianming, primary, Deng, Xianming, primary, Lim, Sang Min, primary, Heynck, Stefanie, primary, Peifer, Martin, primary, Simard, Jeffrey R., primary, Lawrence, Michael S., primary, Onofrio, Robert C., primary, Salvesen, Helga B., primary, Seidel, Danila, primary, Zander, Thomas, primary, Heuckmann, Johannes M., primary, Soltermann, Alex, primary, Moch, Holger, primary, Koker, Mirjam, primary, Leenders, Frauke, primary, Gabler, Franziska, primary, Querings, Silvia, primary, Ansén, Sascha, primary, Brambilla, Elisabeth, primary, Brambilla, Christian, primary, Lorimier, Philippe, primary, Brustugun, Odd Terje, primary, Helland, Åslaug, primary, Petersen, Iver, primary, Clement, Joachim H., primary, Groen, Harry, primary, Timens, Wim, primary, Sietsma, Hannie, primary, Stoelben, Erich, primary, Wolf, Jürgen, primary, Beer, David G., primary, Tsao, Ming Sound, primary, Hanna, Megan, primary, Hatton, Charles, primary, Eck, Michael J., primary, Janne, Pasi A., primary, Johnson, Bruce E., primary, Winckler, Wendy, primary, Greulich, Heidi, primary, Bass, Adam J., primary, Cho, Jeonghee, primary, Rauh, Daniel, primary, Gray, Nathanael S., primary, Wong, Kwok-Kin, primary, Haura, Eric B., primary, Thomas, Roman K., primary, and Meyerson, Matthew, primary

Published
2023
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18. Supplementary Figure Legends 1-7 from Mutations in the DDR2 Kinase Gene Identify a Novel Therapeutic Target in Squamous Cell Lung Cancer

Author

Hammerman, Peter S., primary, Sos, Martin L., primary, Ramos, Alex H., primary, Xu, Chunxiao, primary, Dutt, Amit, primary, Zhou, Wenjun, primary, Brace, Lear E., primary, Woods, Brittany A., primary, Lin, Wenchu, primary, Zhang, Jianming, primary, Deng, Xianming, primary, Lim, Sang Min, primary, Heynck, Stefanie, primary, Peifer, Martin, primary, Simard, Jeffrey R., primary, Lawrence, Michael S., primary, Onofrio, Robert C., primary, Salvesen, Helga B., primary, Seidel, Danila, primary, Zander, Thomas, primary, Heuckmann, Johannes M., primary, Soltermann, Alex, primary, Moch, Holger, primary, Koker, Mirjam, primary, Leenders, Frauke, primary, Gabler, Franziska, primary, Querings, Silvia, primary, Ansén, Sascha, primary, Brambilla, Elisabeth, primary, Brambilla, Christian, primary, Lorimier, Philippe, primary, Brustugun, Odd Terje, primary, Helland, Åslaug, primary, Petersen, Iver, primary, Clement, Joachim H., primary, Groen, Harry, primary, Timens, Wim, primary, Sietsma, Hannie, primary, Stoelben, Erich, primary, Wolf, Jürgen, primary, Beer, David G., primary, Tsao, Ming Sound, primary, Hanna, Megan, primary, Hatton, Charles, primary, Eck, Michael J., primary, Janne, Pasi A., primary, Johnson, Bruce E., primary, Winckler, Wendy, primary, Greulich, Heidi, primary, Bass, Adam J., primary, Cho, Jeonghee, primary, Rauh, Daniel, primary, Gray, Nathanael S., primary, Wong, Kwok-Kin, primary, Haura, Eric B., primary, Thomas, Roman K., primary, and Meyerson, Matthew, primary

Published
2023
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19. Supplementary Figures 1-7 from Mutations in the DDR2 Kinase Gene Identify a Novel Therapeutic Target in Squamous Cell Lung Cancer

Author

Hammerman, Peter S., primary, Sos, Martin L., primary, Ramos, Alex H., primary, Xu, Chunxiao, primary, Dutt, Amit, primary, Zhou, Wenjun, primary, Brace, Lear E., primary, Woods, Brittany A., primary, Lin, Wenchu, primary, Zhang, Jianming, primary, Deng, Xianming, primary, Lim, Sang Min, primary, Heynck, Stefanie, primary, Peifer, Martin, primary, Simard, Jeffrey R., primary, Lawrence, Michael S., primary, Onofrio, Robert C., primary, Salvesen, Helga B., primary, Seidel, Danila, primary, Zander, Thomas, primary, Heuckmann, Johannes M., primary, Soltermann, Alex, primary, Moch, Holger, primary, Koker, Mirjam, primary, Leenders, Frauke, primary, Gabler, Franziska, primary, Querings, Silvia, primary, Ansén, Sascha, primary, Brambilla, Elisabeth, primary, Brambilla, Christian, primary, Lorimier, Philippe, primary, Brustugun, Odd Terje, primary, Helland, Åslaug, primary, Petersen, Iver, primary, Clement, Joachim H., primary, Groen, Harry, primary, Timens, Wim, primary, Sietsma, Hannie, primary, Stoelben, Erich, primary, Wolf, Jürgen, primary, Beer, David G., primary, Tsao, Ming Sound, primary, Hanna, Megan, primary, Hatton, Charles, primary, Eck, Michael J., primary, Janne, Pasi A., primary, Johnson, Bruce E., primary, Winckler, Wendy, primary, Greulich, Heidi, primary, Bass, Adam J., primary, Cho, Jeonghee, primary, Rauh, Daniel, primary, Gray, Nathanael S., primary, Wong, Kwok-Kin, primary, Haura, Eric B., primary, Thomas, Roman K., primary, and Meyerson, Matthew, primary

Published
2023
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20. Supplementary Table 1 from Mutations in the DDR2 Kinase Gene Identify a Novel Therapeutic Target in Squamous Cell Lung Cancer

Author

Hammerman, Peter S., primary, Sos, Martin L., primary, Ramos, Alex H., primary, Xu, Chunxiao, primary, Dutt, Amit, primary, Zhou, Wenjun, primary, Brace, Lear E., primary, Woods, Brittany A., primary, Lin, Wenchu, primary, Zhang, Jianming, primary, Deng, Xianming, primary, Lim, Sang Min, primary, Heynck, Stefanie, primary, Peifer, Martin, primary, Simard, Jeffrey R., primary, Lawrence, Michael S., primary, Onofrio, Robert C., primary, Salvesen, Helga B., primary, Seidel, Danila, primary, Zander, Thomas, primary, Heuckmann, Johannes M., primary, Soltermann, Alex, primary, Moch, Holger, primary, Koker, Mirjam, primary, Leenders, Frauke, primary, Gabler, Franziska, primary, Querings, Silvia, primary, Ansén, Sascha, primary, Brambilla, Elisabeth, primary, Brambilla, Christian, primary, Lorimier, Philippe, primary, Brustugun, Odd Terje, primary, Helland, Åslaug, primary, Petersen, Iver, primary, Clement, Joachim H., primary, Groen, Harry, primary, Timens, Wim, primary, Sietsma, Hannie, primary, Stoelben, Erich, primary, Wolf, Jürgen, primary, Beer, David G., primary, Tsao, Ming Sound, primary, Hanna, Megan, primary, Hatton, Charles, primary, Eck, Michael J., primary, Janne, Pasi A., primary, Johnson, Bruce E., primary, Winckler, Wendy, primary, Greulich, Heidi, primary, Bass, Adam J., primary, Cho, Jeonghee, primary, Rauh, Daniel, primary, Gray, Nathanael S., primary, Wong, Kwok-Kin, primary, Haura, Eric B., primary, Thomas, Roman K., primary, and Meyerson, Matthew, primary

Published
2023
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21. Data from Modeling Genomic Diversity and Tumor Dependency in Malignant Melanoma

Author

Lin, William M., primary, Baker, Alissa C., primary, Beroukhim, Rameen, primary, Winckler, Wendy, primary, Feng, Whei, primary, Marmion, Jennifer M., primary, Laine, Elisabeth, primary, Greulich, Heidi, primary, Tseng, Hsiuyi, primary, Gates, Casey, primary, Hodi, F. Stephen, primary, Dranoff, Glenn, primary, Sellers, William R., primary, Thomas, Roman K., primary, Meyerson, Matthew, primary, Golub, Todd R., primary, Dummer, Reinhard, primary, Herlyn, Meenhard, primary, Getz, Gad, primary, and Garraway, Levi A., primary

Published
2023
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22. Supplementary File 3 from Genome-Wide Functional Synergy between Amplified and Mutated Genes in Human Breast Cancer

Author

Nikolsky, Yuri, primary, Sviridov, Evgeny, primary, Yao, Jun, primary, Dosymbekov, Damir, primary, Ustyansky, Vadim, primary, Kaznacheev, Valery, primary, Dezso, Zoltan, primary, Mulvey, Laura, primary, Macconaill, Laura E., primary, Winckler, Wendy, primary, Serebryiskaya, Tatiana, primary, Nikolskaya, Tatiana, primary, and Polyak, Kornelia, primary

Published
2023
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23. Supplementary File 2 from Genome-Wide Functional Synergy between Amplified and Mutated Genes in Human Breast Cancer

Author

Nikolsky, Yuri, primary, Sviridov, Evgeny, primary, Yao, Jun, primary, Dosymbekov, Damir, primary, Ustyansky, Vadim, primary, Kaznacheev, Valery, primary, Dezso, Zoltan, primary, Mulvey, Laura, primary, Macconaill, Laura E., primary, Winckler, Wendy, primary, Serebryiskaya, Tatiana, primary, Nikolskaya, Tatiana, primary, and Polyak, Kornelia, primary

Published
2023
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24. Supplementary File 1 from Genome-Wide Functional Synergy between Amplified and Mutated Genes in Human Breast Cancer

Author

Nikolsky, Yuri, primary, Sviridov, Evgeny, primary, Yao, Jun, primary, Dosymbekov, Damir, primary, Ustyansky, Vadim, primary, Kaznacheev, Valery, primary, Dezso, Zoltan, primary, Mulvey, Laura, primary, Macconaill, Laura E., primary, Winckler, Wendy, primary, Serebryiskaya, Tatiana, primary, Nikolskaya, Tatiana, primary, and Polyak, Kornelia, primary

Published
2023
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25. Supplementary File 5 from Genome-Wide Functional Synergy between Amplified and Mutated Genes in Human Breast Cancer

Author

Nikolsky, Yuri, primary, Sviridov, Evgeny, primary, Yao, Jun, primary, Dosymbekov, Damir, primary, Ustyansky, Vadim, primary, Kaznacheev, Valery, primary, Dezso, Zoltan, primary, Mulvey, Laura, primary, Macconaill, Laura E., primary, Winckler, Wendy, primary, Serebryiskaya, Tatiana, primary, Nikolskaya, Tatiana, primary, and Polyak, Kornelia, primary

Published
2023
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26. Supplementary File 4 from Genome-Wide Functional Synergy between Amplified and Mutated Genes in Human Breast Cancer

Author

Nikolsky, Yuri, primary, Sviridov, Evgeny, primary, Yao, Jun, primary, Dosymbekov, Damir, primary, Ustyansky, Vadim, primary, Kaznacheev, Valery, primary, Dezso, Zoltan, primary, Mulvey, Laura, primary, Macconaill, Laura E., primary, Winckler, Wendy, primary, Serebryiskaya, Tatiana, primary, Nikolskaya, Tatiana, primary, and Polyak, Kornelia, primary

Published
2023
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27. Supplementary Information from Modeling Genomic Diversity and Tumor Dependency in Malignant Melanoma

Author

Lin, William M., primary, Baker, Alissa C., primary, Beroukhim, Rameen, primary, Winckler, Wendy, primary, Feng, Whei, primary, Marmion, Jennifer M., primary, Laine, Elisabeth, primary, Greulich, Heidi, primary, Tseng, Hsiuyi, primary, Gates, Casey, primary, Hodi, F. Stephen, primary, Dranoff, Glenn, primary, Sellers, William R., primary, Thomas, Roman K., primary, Meyerson, Matthew, primary, Golub, Todd R., primary, Dummer, Reinhard, primary, Herlyn, Meenhard, primary, Getz, Gad, primary, and Garraway, Levi A., primary

Published
2023
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28. Supplementary File 6 from Genome-Wide Functional Synergy between Amplified and Mutated Genes in Human Breast Cancer

Author

Nikolsky, Yuri, primary, Sviridov, Evgeny, primary, Yao, Jun, primary, Dosymbekov, Damir, primary, Ustyansky, Vadim, primary, Kaznacheev, Valery, primary, Dezso, Zoltan, primary, Mulvey, Laura, primary, Macconaill, Laura E., primary, Winckler, Wendy, primary, Serebryiskaya, Tatiana, primary, Nikolskaya, Tatiana, primary, and Polyak, Kornelia, primary

Published
2023
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29. Materials and Methods, Legends, Tables and Figures from Genome-Wide Functional Synergy between Amplified and Mutated Genes in Human Breast Cancer

Author

Nikolsky, Yuri, primary, Sviridov, Evgeny, primary, Yao, Jun, primary, Dosymbekov, Damir, primary, Ustyansky, Vadim, primary, Kaznacheev, Valery, primary, Dezso, Zoltan, primary, Mulvey, Laura, primary, Macconaill, Laura E., primary, Winckler, Wendy, primary, Serebryiskaya, Tatiana, primary, Nikolskaya, Tatiana, primary, and Polyak, Kornelia, primary

Published
2023
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30. Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features

Author

Pitt, Jason J., Riester, Markus, Zheng, Yonglan, Yoshimatsu, Toshio F., Sanni, Ayodele, Oluwasola, Olayiwola, Veloso, Artur, Labrot, Emma, Wang, Shengfeng, Odetunde, Abayomi, Ademola, Adeyinka, Okedere, Babajide, Mahan, Scott, Leary, Rebecca, Macomber, Maura, Ajani, Mustapha, Johnson, Ryan S., Fitzgerald, Dominic, Grundstad, A. Jason, Tuteja, Jigyasa H., Khramtsova, Galina, Zhang, Jing, Sveen, Elisabeth, Hwang, Bryce, Clayton, Wendy, Nkwodimmah, Chibuzor, Famooto, Bisola, Obasi, Esther, Aderoju, Victor, Oludara, Mobolaji, Omodele, Folusho, Akinyele, Odunayo, Adeoye, Adewunmi, Ogundiran, Temidayo, Babalola, Chinedum, MacIsaac, Kenzie, Popoola, Abiodun, Morrissey, Michael P., Chen, Lin S., Wang, Jiebiao, Olopade, Christopher O., Falusi, Adeyinka G., Winckler, Wendy, Haase, Kerstin, Van Loo, Peter, Obafunwa, John, Papoutsakis, Dimitris, Ojengbede, Oladosu, Weber, Barbara, Ibrahim, Nasiru, White, Kevin P., Huo, Dezheng, Olopade, Olufunmilayo I., and Barretina, Jordi

Published
2018
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31. Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling

Author

Wawer, Mathias J., Li, Kejie, Gustafsdottir, Sigrun M., Ljos, Vebjorn, Bodycombe, Nicole E., Marton, Melissa A., Sokolnicki, Katherine L., Bray, Mark-Anthony, Kemp, Melissa M., Winchester, Ellen, Taylor, Bradley, Grant, George B., Hon, C. Suk-Yee, Duvall, Jeremy R., Wilson, J. Anthony, Bittker, Joshua A., Dančík, Vlado, Narayan, Rajiv, Subramanian, Aravind, Winckler, Wendy, Golub, Todd R., Carpenter, Anne E., Shamji, Alykhan F., Schreiber, Stuart L., and Clemons, Paul A.

Published
2014

32. Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

Author

Barretina, Jordi, Caponigro, Giordano, Stransky, Nicolas, Venkatesan, Kavitha, Margolin, Adam A., Kim, Sungjoon, Wilson, Christopher J., Lehár, Joseph, Kryukov, Gregory V., Sonkin, Dmitriy, Reddy, Anupama, Liu, Manway, Murray, Lauren, Berger, Michael F., Monahan, John E., Morais, Paula, Meltzer, Jodi, Korejwa, Adam, Jané-Valbuena, Judit, Mapa, Felipa A., Thibault, Joseph, Bric-Furlong, Eva, Raman, Pichai, Shipway, Aaron, Engels, Ingo H., Cheng, Jill, Yu, Guoying K., Yu, Jianjun, Aspesi, Jr, Peter, de Silva, Melanie, Jagtap, Kalpana, Jones, Michael D., Wang, Li, Hatton, Charles, Palescandolo, Emanuele, Gupta, Supriya, Mahan, Scott, Sougnez, Carrie, Onofrio, Robert C., Liefeld, Ted, MacConaill, Laura, Winckler, Wendy, Reich, Michael, Li, Nanxin, Mesirov, Jill P., Gabriel, Stacey B., Getz, Gad, Ardlie, Kristin, Chan, Vivien, Myer, Vic E., Weber, Barbara L., Porter, Jeff, Warmuth, Markus, Finan, Peter, Harris, Jennifer L., Meyerson, Matthew, Golub, Todd R., Morrissey, Michael P., Sellers, William R., Schlegel, Robert, and Garraway, Levi A.

Published
2019
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33. Novel and accurate measurement of differential protease activity in diagnosed HCC patients compared to non-HCC cirrhotic patients

Author

Singal, Amit, primary, Tran, Tram, additional, Holmes, Ben, additional, Gulka, Chris, additional, Myaskovsky, Anatoly, additional, Shepard, Andrea, additional, Rowe, Mackenzie, additional, Cazanave, Sophie, additional, Touti, Faycal, additional, Lee, Jina, additional, Balbin, Alejandro, additional, and Winckler, Wendy, additional

Published
2022
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35. Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2

Author

Greulich, Heidi, Kaplan, Bethany, Mertins, Philipp, Chen, Tzu-Hsiu, Tanaka, Kumiko E., Yun, Cai-Hong, Zhang, Xiaohong, Lee, Se-Hoon, Cho, Jeonghee, Ambrogio, Lauren, Liao, Rachel, Imielinski, Marcin, Banerji, Shantanu, Berger, Alice H., Lawrence, Michael S., Zhang, Jinghui, Pho, Nam H., Walker, Sarah R., Winckler, Wendy, Getz, Gad, Frank, David, Hahn, William C., Eck, Michael J., Mani, D. R., Jaffe, Jacob D., Carr, Steven A., Wong, Kwok-Kin, and Meyerson, Matthew

Published
2012

36. The Mutational Landscape of Head and Neck Squamous Cell Carcinoma

Author

Stransky, Nicolas, Egloff, Ann Marie, Tward, Aaron D., Kostic, Aleksandar D., Cibulskis, Kristian, Sivachenko, Andrey, Kryukov, Gregory V., Lawrence, Michael S., Sougnez, Carrie, McKenna, Aaron, Shefler, Erica, Ramos, Alex H., Stojanov, Petar, Carter, Scott L., Voet, Douglas, Cortés, Maria L., Auclair, Daniel, Berger, Michael F., Saksena, Gordon, Guiducci, Candace, Onofrio, Robert C., Parkin, Melissa, Romkes, Marjorie, Weissfeld, Joel L., Seethala, Raja R., Wang, Lin, Rangel-Escareño, Claudia, Fernandez-Lopez, Juan Carlos, Hidalgo-Miranda, Alfredo, Melendez-Zajgla, Jorge, Winckler, Wendy, Ardlie, Kristin, Gabriel, Stacey B., Meyerson, Matthew, Lander, Eric S., Getz, Gad, Golub, Todd R., Garraway, Levi A., and Grandis, Jennifer R.

Published
2011
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37. Drug-Sensitive FGFR2 Mutations in Endometrial Carcinoma

Author

Dutt, Amit, Salvesen, Helga B., Chen, Tzu-Hsiu, Ramos, Alex H., Onofrio, Robert C., Hatton, Charlie, Nicoletti, Richard, Winckler, Wendy, Grewal, Rupinder, Hanna, Megan, Wyhs, Nicolas, Ziaugra, Liuda, Richter, Daniel J., Trovik, Jone, Engelsen, Ingeborg B., Stefansson, Ingunn M., Fennell, Tim, Cibulskis, Kristian, Zody, Michael C., Akslen, Lars A., Gabriel, Stacey, Wong, Kwok-Kin, Sellers, William R., Meyerson, Matthew, and Greulich, Heidi

Published
2008
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38. Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

Author

Verhaak, Roel G.W., Hoadley, Katherine A., Purdom, Elizabeth, Wang, Victoria, Qi, Yuan, Wilkerson, Matthew D., Miller, C. Ryan, Ding, Li, Golub, Todd, Mesirov, Jill P., Alexe, Gabriele, Lawrence, Michael, O'Kelly, Michael, Tamayo, Pablo, Weir, Barbara A., Gabriel, Stacey, Winckler, Wendy, Gupta, Supriya, Jakkula, Lakshmi, Feiler, Heidi S., Hodgson, J. Graeme, James, C. David, Sarkaria, Jann N., Brennan, Cameron, Kahn, Ari, Spellman, Paul T., Wilson, Richard K., Speed, Terence P., Gray, Joe W., Meyerson, Matthew, Getz, Gad, Perou, Charles M., and Hayes, D. Neil

Published
2010
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39. Peptide-based urinary monitoring of fibrotic nonalcoholic steatohepatitis by mass-barcoded activity-based sensors

Author

Cazanave, Sophie C., primary, Warren, Andrew D., additional, Pacula, Maciej, additional, Touti, Fayçal, additional, Zagorska, Anna, additional, Gural, Nil, additional, Huang, Eric K., additional, Sherman, Sarah, additional, Cheema, Mehar, additional, Ibarra, Sabrina, additional, Bates, Jamie, additional, Billin, Andrew N., additional, Liles, John T., additional, Budas, Grant R., additional, Breckenridge, David G., additional, Tiniakos, Dina, additional, Ratziu, Vlad, additional, Daly, Ann K., additional, Govaere, Olivier, additional, Anstee, Quentin M., additional, Gelrud, Louis, additional, Luther, Jay, additional, Chung, Raymond T., additional, Corey, Kathleen E., additional, Winckler, Wendy, additional, Bhatia, Sangeeta, additional, and Kwong, Gabriel A., additional

Published
2021
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40. Epidermal growth factor receptor inhibition attenuates liver fibrosis and development of hepatocellular carcinoma

Author

Fuchs, Bryan C., Hoshida, Yujin, Fujii, Tsutomu, Wei, Lan, Yamada, Suguru, Lauwers, Gregory Y., McGinn, Christopher M., DePeralta, Danielle K., Chen, Xintong, Kuroda, Toshihiko, Lanuti, Michael, Schmitt, Anthony D., Gupta, Supriya, Crenshaw, Andrew, Onofrio, Robert, Taylor, Bradley, Winckler, Wendy, Bardeesy, Nabeel, Caravan, Peter, Golub, Todd R., and Tanabe, Kenneth K.

Published
2014
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41. Predicting drug susceptibility of non--small cell lung cancers based on genetic lesions

Author

Sos, Martin L., Michel, Kathrin, Zander, Thomas, Weiss, Jonathan, Frommolt, Peter, Peifer, Martin, Li, Danan, Ullrich, Roland, Koker, Mirjam, Fischer, Florian, Shimamura, Takeshi, Rauh, Daniel, Mermel, Craig, Fischer, Stefanie, Stuckrath, Isabel, Heynck, Stefanie, Beroukhim, Rameen, Lin, William, Winckler, Wendy, Shah, Kinjal, LaFramboise, Thomas, Moriarty, Whei F., Hanna, Megan, Tolosi, Laura, Rahnenfuhrer, Jorg, Verhaak, Roel, Chiang, Derek, Getz, Gad, Hellmich, Martin, Wolf, Jurgen, Girard, Luc, Peyton, Michael, Weir, Barbara A., Chen, Tzu-Hsiu, Greulich, Heidi, Barretina, Jordi, Shapiro, Geoffrey I., Garraway, Levi A., Gazdar, Adi F., Minna, John D., Meyerson, Matthew, Wong, Kwok-Kin, and Thomas, Roman K.

Subjects
Gene mutations -- Health aspects, Genetic susceptibility -- Research, Heat shock proteins -- Health aspects, Heat shock proteins -- Genetic aspects, Heat shock proteins -- Research, Lung cancer, Non-small cell -- Risk factors, Lung cancer, Non-small cell -- Genetic aspects, Lung cancer, Non-small cell -- Care and treatment, Lung cancer, Non-small cell -- Research
Abstract

Somatic genetic alterations in cancers have been linked with response to targeted therapeutics by creation of specific dependency on activated oncogenic signaling pathways. However, no tools currently exist to systematically connect such genetic lesions to therapeutic vulnerability. We have therefore developed a genomics approach to identify lesions associated with therapeutically relevant oncogene dependency. Using integrated genomic profiling, we have demonstrated that the genomes of a large panel of human non--small cell lung cancer (NSCLC) cell lines are highly representative of those of primary NSCLC tumors. Using cell-based compound screening coupled with diverse computational approaches to integrate orthogonal genomic and biochemical data sets, we identified molecular and genomic predictors of therapeutic response to clinically relevant compounds. Using this approach, we showed that v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations confer enhanced Hsp90 dependency and validated this finding in mice with KRAS-driven lung adenocarcinoma, as these mice exhibited dramatic tumor regression when treated with an Hsp90 inhibitor. In addition, we found that cells with copy number enhancement of v-abl Abelson murine leukemia viral oncogene homolog 2 (ABL2) and ephrin receptor kinase and v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian) (SRC) kinase family genes were exquisitely sensitive to treatment with the SRC/ABL inhibitor dasatinib, both in vitro and when it xenografted into mice. Thus, genomically annotated cell-line collections may help translate cancer genomics information into clinical practice by defining critical pathway dependencies amenable to therapeutic inhibition., Introduction The dynamics of ongoing efforts to fully annotate the genomes of all major cancer types are reminiscent of those of the Human Genome Project. The analysis of somatic gene [...]

Published
2009

42. Somatic mutations affect key pathways in lung adenocarcinoma

Author

Ding, Li, Getz, Gad, Wheeler, David A., Mardis, Elaine R., McLellan, Michael D., Cibulskis, Kristian, Sougnez, Carrie, Greulich, Heidi, Muzny, Donna M., Morgan, Margaret B., Fulton, Lucinda, Fulton, Robert S., Zhang, Qunyuan, Wendl, Michael C., Lawrence, Michael S., Larson, David E., Chen, Ken, Dooling, David J., Sabo, Aniko, Hawes, Alicia C., Shen, Hua, Jhangiani, Shalini N., Lewis, Lora R., Hall, Otis, Zhu, Yiming, Mathew, Tittu, Ren, Yanru, Yao, Jiqiang, Scherer, Steven E., Clerc, Kerstin, Metcalf, Ginger A., Ng, Brian, Milosavljevic, Aleksandar, Gonzalez-Garay, Manuel L., Osborne, John R., Meyer, Rick, Shi, Xiaoqi, Tang, Yuzhu, Koboldt, Daniel C., Lin, Ling, Abbott, Rachel, Miner, Tracie L., Pohl, Craig, Fewell, Ginger, Haipek, Carrie, Schmidt, Heather, Dunford-Shore, Brian H., Kraja, Aldi, Crosby, Seth D., Sawyer, Christopher S., Vickery, Tammi, Sander, Sacha, Robinson, Jody, Winckler, Wendy, Baldwin, Jennifer, Chirieac, Lucian R., Dutt, Amit, Fennell, Tim, Hanna, Megan, Johnson, Bruce E., Onofrio, Robert C., Thomas, Roman K., Tonon, Giovanni, Weir, Barbara A., Zhao, Xiaojun, Ziaugra, Liuda, Zody, Michael C., Giordano, Thomas, Orringer, Mark B., Roth, Jack A., Spitz, Margaret R., Wistuba, Ignacio I., Ozenberger, Bradley, Good, Peter J., Chang, Andrew C., Beer, David G., Watson, Mark A., Ladanyi, Marc, Broderick, Stephen, Yoshizawa, Akihiko, Travis, William D., Pao, William, Province, Michael A., Weinstock, George M., Varmus, Harold E., Gabriel, Stacey B., Lander, Eric S., Gibbs, Richard A., Meyerson, Matthew, and Wilson, Richard K.

Subjects
Gene mutations -- Research -- Physiological aspects -- Genetic aspects, Nucleotide sequencing -- Research -- Physiological aspects -- Genetic aspects, Adenocarcinoma -- Genetic aspects -- Research -- Care and treatment -- Prognosis -- Diagnosis, DNA sequencing -- Research -- Physiological aspects -- Genetic aspects, Lung cancer -- Genetic aspects -- Research -- Care and treatment -- Diagnosis -- Prognosis, Environmental issues, Science and technology, Zoology and wildlife conservation, Diagnosis, Care and treatment, Physiological aspects, Genetic aspects, Research, Prognosis
Abstract

Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well-classified primary tumours. Here we report the results of a collaborative study to discover somatic mutations [...]

Published
2008

43. Mutational heterogeneity in cancer and the search for new cancer-associated genes

Author

Lawrence, Michael S., Stojanov, Petar, Polak, Paz, Kryukov, Gregory V., Cibulskis, Kristian, Sivachenko, Andrey, Carter, Scott L., Stewart, Chip, Mermel, Craig H., Roberts, Steven A., Kiezun, Adam, Hammerman, Peter S., McKenna, Aaron, Drier, Yotam, Zou, Lihua, Ramos, Alex H., Pugh, Trevor J., Stransky, Nicolas, Helman, Elena, Kim, Jaegil, Sougnez, Carrie, Ambrogio, Lauren, Nickerson, Elizabeth, Shefler, Erica, Cortés, Maria L., Auclair, Daniel, Saksena, Gordon, Voet, Douglas, Noble, Michael, DiCara, Daniel, Lin, Pei, Lichtenstein, Lee, Heiman, David I., Fennell, Timothy, Imielinski, Marcin, Hernandez, Bryan, Hodis, Eran, Baca, Sylvan, Dulak, Austin M., Lohr, Jens, Landau, Dan-Avi, Wu, Catherine J., Melendez-Zajgla, Jorge, Hidalgo-Miranda, Alfredo, Koren, Amnon, McCarroll, Steven A., Mora, Jaume, Lee, Ryan S., Crompton, Brian, Onofrio, Robert, Parkin, Melissa, Winckler, Wendy, Ardlie, Kristin, Gabriel, Stacey B., Roberts, Charles W. M., Biegel, Jaclyn A., Stegmaier, Kimberly, Bass, Adam J., Garraway, Levi A., Meyerson, Matthew, Golub, Todd R., Gordenin, Dmitry A., Sunyaev, Shamil, Lander, Eric S., and Getz, Gad

Published
2013
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44. Comprehensive molecular portraits of human breast tumours

Author

Koboldt, Daniel C., Fulton, Robert S., McLellan, Michael D., Schmidt, Heather, Kalicki-Veizer, Joelle, McMichael, Joshua F., Fulton, Lucinda L., Dooling, David J., Ding, Li, Mardis, Elaine R., Wilson, Richard K., Ally, Adrian, Balasundaram, Miruna, Butterfield, Yaron S. N., Carlsen, Rebecca, Carter, Candace, Chu, Andy, Chuah, Eric, Chun, Hye-Jung E., Coope, Robin J. N., Dhalla, Noreen, Guin, Ranabir, Hirst, Carrie, Hirst, Martin, Holt, Robert A., Lee, Darlene, Li, Haiyan I., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Pleasance, Erin, Gordon Robertson, A., Schein, Jacqueline E., Shafiei, Arash, Sipahimalani, Payal, Slobodan, Jared R., Stoll, Dominik, Tam, Angela, Thiessen, Nina, Varhol, Richard J., Wye, Natasja, Zeng, Thomas, Zhao, Yongjun, Birol, Inanc, Jones, Steven J. M., Marra, Marco A., Cherniack, Andrew D., Saksena, Gordon, Onofrio, Robert C., Pho, Nam H., Carter, Scott L., Schumacher, Steven E., Tabak, Barbara, Hernandez, Bryan, Gentry, Jeff, Nguyen, Huy, Crenshaw, Andrew, Ardlie, Kristin, Beroukhim, Rameen, Winckler, Wendy, Getz, Gad, Gabriel, Stacey B., Meyerson, Matthew, Chin, Lynda, Park, Peter J., Kucherlapati, Raju, Hoadley, Katherine A., Todd Auman, J., Fan, Cheng, Turman, Yidi J., Shi, Yan, Li, Ling, Topal, Michael D., He, Xiaping, Chao, Hann-Hsiang, Prat, Aleix, Silva, Grace O., Iglesia, Michael D., Zhao, Wei, Usary, Jerry, Berg, Jonathan S., Adams, Michael, Booker, Jessica, Wu, Junyuan, Gulabani, Anisha, Bodenheimer, Tom, Hoyle, Alan P., Simons, Janae V., Soloway, Matthew G., Mose, Lisle E., Jefferys, Stuart R., Balu, Saianand, Parker, Joel S., Neil Hayes, D., Perou, Charles M., Malik, Simeen, Mahurkar, Swapna, Shen, Hui, Weisenberger, Daniel J., Triche, Timothy, Jr, Lai, Phillip H., Bootwalla, Moiz S., Maglinte, Dennis T., Berman, Benjamin P., Van Den Berg, David J., Baylin, Stephen B., Laird, Peter W., Creighton, Chad J., Donehower, Lawrence A., Noble, Michael, Voet, Doug, Gehlenborg, Nils, DiCara, Daniel, Zhang, Juinhua, Zhang, Hailei, Wu, Chang-Jiun, Liu, Spring Yingchun, Lawrence, Michael S., Zou, Lihua, Sivachenko, Andrey, Lin, Pei, Stojanov, Petar, Jing, Rui, Cho, Juok, Sinha, Raktim, Park, Richard W., Nazaire, Marc-Danie, Robinson, Jim, Thorvaldsdottir, Helga, Mesirov, Jill, Reynolds, Sheila, Kreisberg, Richard B., Bernard, Brady, Bressler, Ryan, Erkkila, Timo, Lin, Jake, Thorsson, Vesteinn, Zhang, Wei, Shmulevich, Ilya, Ciriello, Giovanni, Weinhold, Nils, Schultz, Nikolaus, Gao, Jianjiong, Cerami, Ethan, Gross, Benjamin, Jacobsen, Anders, Sinha, Rileen, Arman Aksoy, B., Antipin, Yevgeniy, Reva, Boris, Shen, Ronglai, Taylor, Barry S., Ladanyi, Marc, Sander, Chris, Anur, Pavana, Spellman, Paul T., Lu, Yiling, Liu, Wenbin, Verhaak, Roel R. G., Mills, Gordon B., Akbani, Rehan, Zhang, Nianxiang, Broom, Bradley M., Casasent, Tod D., Wakefield, Chris, Unruh, Anna K., Baggerly, Keith, Coombes, Kevin, Weinstein, John N., Haussler, David, Benz, Christopher C., Stuart, Joshua M., Benz, Stephen C., Zhu, Jingchun, Szeto, Christopher C., Scott, Gary K., Yau, Christina, Paull, Evan O., Carlin, Daniel, Wong, Christopher, Sokolov, Artem, Thusberg, Janita, Mooney, Sean, Ng, Sam, Goldstein, Theodore C., Ellrott, Kyle, Grifford, Mia, Wilks, Christopher, Ma, Singer, Craft, Brian, Yan, Chunhua, Hu, Ying, Meerzaman, Daoud, Gastier-Foster, Julie M., Bowen, Jay, Ramirez, Nilsa C., Black, Aaron D., Pyatt, Robert E., White, Peter, Zmuda, Erik J., Frick, Jessica, Lichtenberg, Tara M., Brookens, Robin, George, Myra M., Gerken, Mark A., Harper, Hollie A., Leraas, Kristen M., Wise, Lisa J., Tabler, Teresa R., McAllister, Cynthia, Barr, Thomas, Hart-Kothari, Melissa, Tarvin, Katie, Saller, Charles, Sandusky, George, Mitchell, Colleen, Iacocca, Mary V., Brown, Jennifer, Rabeno, Brenda, Czerwinski, Christine, Petrelli, Nicholas, Dolzhansky, Oleg, Abramov, Mikhail, Voronina, Olga, Potapova, Olga, Marks, Jeffrey R., Suchorska, Wiktoria M., Murawa, Dawid, Kycler, Witold, Ibbs, Matthew, Korski, Konstanty, Spychała, Arkadiusz, Murawa, Paweł, Brzeziński, Jacek J., Perz, Hanna, Łaźniak, Radosław, Teresiak, Marek, Tatka, Honorata, Leporowska, Ewa, Bogusz-Czerniewicz, Marta, Malicki, Julian, Mackiewicz, Andrzej, Wiznerowicz, Maciej, Van Le, Xuan, Kohl, Bernard, Viet Tien, Nguyen, Thorp, Richard, Van Bang, Nguyen, Sussman, Howard, Duc Phu, Bui, Hajek, Richard, Phi Hung, Nguyen, Viet The Phuong, Tran, Quyet Thang, Huynh, Zaki Khan, Khurram, Penny, Robert, Mallery, David, Curley, Erin, Shelton, Candace, Yena, Peggy, Ingle, James N., Couch, Fergus J., Lingle, Wilma L., King, Tari A., Maria Gonzalez-Angulo, Ana, Dyer, Mary D., Liu, Shuying, Meng, Xiaolong, Patangan, Modesto, Waldman, Frederic, Stöppler, Hubert, Kimryn Rathmell, W., Thorne, Leigh, Huang, Mei, Boice, Lori, Hill, Ashley, Morrison, Carl, Gaudioso, Carmelo, Bshara, Wiam, Daily, Kelly, Egea, Sophie C., Pegram, Mark D., Gomez-Fernandez, Carmen, Dhir, Rajiv, Bhargava, Rohit, Brufsky, Adam, Shriver, Craig D., Hooke, Jeffrey A., Leigh Campbell, Jamie, Mural, Richard J., Hu, Hai, Somiari, Stella, Larson, Caroline, Deyarmin, Brenda, Kvecher, Leonid, Kovatich, Albert J., Ellis, Matthew J., Stricker, Thomas, White, Kevin, Olopade, Olufunmilayo, Luo, Chunqing, Chen, Yaqin, Bose, Ron, Chang, Li-Wei, Beck, Andrew H., Pihl, Todd, Jensen, Mark, Sfeir, Robert, Kahn, Ari, Chu, Anna, Kothiyal, Prachi, Wang, Zhining, Snyder, Eric, Pontius, Joan, Ayala, Brenda, Backus, Mark, Walton, Jessica, Baboud, Julien, Berton, Dominique, Nicholls, Matthew, Srinivasan, Deepak, Raman, Rohini, Girshik, Stanley, Kigonya, Peter, Alonso, Shelley, Sanbhadti, Rashmi, Barletta, Sean, Pot, David, Sheth, Margi, Demchok, John A., Mills Shaw, Kenna R., Yang, Liming, Eley, Greg, Ferguson, Martin L., Tarnuzzer, Roy W., Zhang, Jiashan, Dillon, Laura A. L., Buetow, Kenneth, Fielding, Peter, Ozenberger, Bradley A., Guyer, Mark S., Sofia, Heidi J., and Palchik, Jacqueline D.

Published
2012
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45. Comprehensive molecular characterization of human colon and rectal cancer

Author

Muzny, Donna M., Bainbridge, Matthew N., Chang, Kyle, Dinh, Huyen H., Drummond, Jennifer A., Fowler, Gerald, Kovar, Christie L., Lewis, Lora R., Morgan, Margaret B., Newsham, Irene F., Reid, Jeffrey G., Santibanez, Jireh, Shinbrot, Eve, Trevino, Lisa R., Wu, Yuan-Qing, Wang, Min, Gunaratne, Preethi, Donehower, Lawrence A., Creighton, Chad J., Wheeler, David A., Gibbs, Richard A., Lawrence, Michael S., Voet, Douglas, Jing, Rui, Cibulskis, Kristian, Sivachenko, Andrey, Stojanov, Petar, McKenna, Aaron, Lander, Eric S., Gabriel, Stacey, Getz, Gad, Ding, Li, Fulton, Robert S., Koboldt, Daniel C., Wylie, Todd, Walker, Jason, Dooling, David J., Fulton, Lucinda, Delehaunty, Kim D., Fronick, Catrina C., Demeter, Ryan, Mardis, Elaine R., Wilson, Richard K., Chu, Andy, Chun, Hye-Jung E., Mungall, Andrew J., Pleasance, Erin, Robertson, Gordon A., Stoll, Dominik, Balasundaram, Miruna, Birol, Inanc, Butterfield, Yaron S. N., Chuah, Eric, Coope, Robin J. N., Dhalla, Noreen, Guin, Ranabir, Hirst, Carrie, Hirst, Martin, Holt, Robert A., Lee, Darlene, Li, Haiyan I., Mayo, Michael, Moore, Richard A., Schein, Jacqueline E., Slobodan, Jared R., Tam, Angela, Thiessen, Nina, Varhol, Richard, Zeng, Thomas, Zhao, Yongjun, Jones, Steven J. M., Marra, Marco A., Bass, Adam J., Ramos, Alex H., Saksena, Gordon, Cherniack, Andrew D., Schumacher, Stephen E., Tabak, Barbara, Carter, Scott L., Pho, Nam H., Nguyen, Huy, Onofrio, Robert C., Crenshaw, Andrew, Ardlie, Kristin, Beroukhim, Rameen, Winckler, Wendy, Meyerson, Matthew, Protopopov, Alexei, Zhang, Juinhua, Hadjipanayis, Angela, Lee, Eunjung, Xi, Ruibin, Yang, Lixing, Ren, Xiaojia, Zhang, Hailei, Sathiamoorthy, Narayanan, Shukla, Sachet, Chen, Peng-Chieh, Haseley, Psalm, Xiao, Yonghong, Lee, Semin, Seidman, Jonathan, Chin, Lynda, Park, Peter J., Kucherlapati, Raju, Auman, Todd J., Hoadley, Katherine A., Du, Ying, Wilkerson, Matthew D., Shi, Yan, Liquori, Christina, Meng, Shaowu, Li, Ling, Turman, Yidi J., Topal, Michael D., Tan, Donghui, Waring, Scot, Buda, Elizabeth, Walsh, Jesse, Jones, Corbin D., Mieczkowski, Piotr A., Singh, Darshan, Wu, Junyuan, Gulabani, Anisha, Dolina, Peter, Bodenheimer, Tom, Hoyle, Alan P., Simons, Janae V., Soloway, Matthew, Mose, Lisle E., Jefferys, Stuart R., Balu, Saianand, O’Connor, Brian D., Prins, Jan F., Chiang, Derek Y., Hayes, Neil D., Perou, Charles M., Hinoue, Toshinori, Weisenberger, Daniel J., Maglinte, Dennis T., Pan, Fei, Berman, Benjamin P., Van Den Berg, David J., Shen, Hui, Triche, Timothy, Jr, Baylin, Stephen B., Laird, Peter W., Noble, Michael, Voet, Doug, Gehlenborg, Nils, DiCara, Daniel, Wu, Chang-Jiun, Yingchun Liu, Spring, Zhou, Lihua, Lin, Pei, Park, Richard W., Nazaire, Marc-Danie, Robinson, Jim, Thorvaldsdottir, Helga, Mesirov, Jill, Thorsson, Vesteinn, Reynolds, Sheila M., Bernard, Brady, Kreisberg, Richard, Lin, Jake, Iype, Lisa, Bressler, Ryan, Erkkilä, Timo, Gundapuneni, Madhumati, Liu, Yuexin, Norberg, Adam, Robinson, Tom, Yang, Da, Zhang, Wei, Shmulevich, Ilya, de Ronde, Jorma J., Schultz, Nikolaus, Cerami, Ethan, Ciriello, Giovanni, Goldberg, Arthur P., Gross, Benjamin, Jacobsen, Anders, Gao, Jianjiong, Kaczkowski, Bogumil, Sinha, Rileen, Aksoy, Arman B., Antipin, Yevgeniy, Reva, Boris, Shen, Ronglai, Taylor, Barry S., Chan, Timothy A., Ladanyi, Marc, Sander, Chris, Akbani, Rehan, Zhang, Nianxiang, Broom, Bradley M., Casasent, Tod, Unruh, Anna, Wakefield, Chris, Hamilton, Stanley R., Cason, Craig R., Baggerly, Keith A., Weinstein, John N., Haussler, David, Benz, Christopher C., Stuart, Joshua M., Benz, Stephen C., Sanborn, Zachary J., Vaske, Charles J., Zhu, Jingchun, Szeto, Christopher, Scott, Gary K., Yau, Christina, Ng, Sam, Goldstein, Ted, Ellrott, Kyle, Collisson, Eric, Cozen, Aaron E., Zerbino, Daniel, Wilks, Christopher, Craft, Brian, Spellman, Paul, Penny, Robert, Shelton, Troy, Hatfield, Martha, Morris, Scott, Yena, Peggy, Shelton, Candace, Sherman, Mark, Paulauskis, Joseph, Gastier-Foster, Julie M., Bowen, Jay, Ramirez, Nilsa C., Black, Aaron, Pyatt, Robert, Wise, Lisa, White, Peter, Bertagnolli, Monica, Brown, Jen, Chu, Gerald C., Czerwinski, Christine, Denstman, Fred, Dhir, Rajiv, Dörner, Arnulf, Fuchs, Charles S., Guillem, Jose G., Iacocca, Mary, Juhl, Hartmut, Kaufman, Andrew, Kohl, Bernard, III, Van Le, Xuan, Mariano, Maria C., Medina, Elizabeth N., Meyers, Michael, Nash, Garrett M., Paty, Phillip B., Petrelli, Nicholas, Rabeno, Brenda, Richards, William G., Solit, David, Swanson, Pat, Temple, Larissa, Tepper, Joel E., Thorp, Richard, Vakiani, Efsevia, Weiser, Martin R., Willis, Joseph E., Witkin, Gary, Zeng, Zhaoshi, Zinner, Michael J., Zornig, Carsten, Jensen, Mark A., Sfeir, Robert, Kahn, Ari B., Chu, Anna L., Kothiyal, Prachi, Wang, Zhining, Snyder, Eric E., Pontius, Joan, Pihl, Todd D., Ayala, Brenda, Backus, Mark, Walton, Jessica, Whitmore, Jon, Baboud, Julien, Berton, Dominique L., Nicholls, Matthew C., Srinivasan, Deepak, Raman, Rohini, Girshik, Stanley, Kigonya, Peter A., Alonso, Shelley, Sanbhadti, Rashmi N., Barletta, Sean P., Greene, John M., Pot, David A., Mills Shaw, Kenna R., Dillon, Laura A. L., Buetow, Ken, Davidsen, Tanja, Demchok, John A., Eley, Greg, Ferguson, Martin, Fielding, Peter, Schaefer, Carl, Sheth, Margi, Yang, Liming, Guyer, Mark S., Ozenberger, Bradley A., Palchik, Jacqueline D., Peterson, Jane, Sofia, Heidi J., and Thomson, Elizabeth

Published
2012
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47. Melanoma genome sequencing reveals frequent PREX2 mutations

Author

Berger, Michael F., Hodis, Eran, Heffernan, Timothy P., Deribe, Yonathan Lissanu, Lawrence, Michael S., Protopopov, Alexei, Ivanova, Elena, Watson, Ian R., Nickerson, Elizabeth, Ghosh, Papia, Zhang, Hailei, Zeid, Rhamy, Ren, Xiaojia, Cibulskis, Kristian, Sivachenko, Andrey Y., Wagle, Nikhil, Sucker, Antje, Sougnez, Carrie, Onofrio, Robert, Ambrogio, Lauren, Auclair, Daniel, Fennell, Timothy, Carter, Scott L., Drier, Yotam, Stojanov, Petar, Singer, Meredith A., Voet, Douglas, Jing, Rui, Saksena, Gordon, Barretina, Jordi, Ramos, Alex H., Pugh, Trevor J., Stransky, Nicolas, Parkin, Melissa, Winckler, Wendy, Mahan, Scott, Ardlie, Kristin, Baldwin, Jennifer, Wargo, Jennifer, Schadendorf, Dirk, Meyerson, Matthew, Gabriel, Stacey B., Golub, Todd R., Wagner, Stephan N., Lander, Eric S., Getz, Gad, Chin, Lynda, and Garraway, Levi A.

Published
2012
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48. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

Author

Barretina, Jordi, Caponigro, Giordano, Stransky, Nicolas, Venkatesan, Kavitha, Margolin, Adam A., Kim, Sungjoon, Wilson, Christopher J., Lehár, Joseph, Kryukov, Gregory V., Sonkin, Dmitriy, Reddy, Anupama, Liu, Manway, Murray, Lauren, Berger, Michael F., Monahan, John E., Morais, Paula, Meltzer, Jodi, Korejwa, Adam, Jané-Valbuena, Judit, Mapa, Felipa A., Thibault, Joseph, Bric-Furlong, Eva, Raman, Pichai, Shipway, Aaron, Engels, Ingo H., Cheng, Jill, Yu, Guoying K., Yu, Jianjun, Aspesi, Peter, de Silva, Melanie, Jagtap, Kalpana, Jones, Michael D., Wang, Li, Hatton, Charles, Palescandolo, Emanuele, Gupta, Supriya, Mahan, Scott, Sougnez, Carrie, Onofrio, Robert C., Liefeld, Ted, MacConaill, Laura, Winckler, Wendy, Reich, Michael, Li, Nanxin, Mesirov, Jill P., Gabriel, Stacey B., Getz, Gad, Ardlie, Kristin, Chan, Vivien, Myer, Vic E., Weber, Barbara L., Porter, Jeff, Warmuth, Markus, Finan, Peter, Harris, Jennifer L., Meyerson, Matthew, Golub, Todd R., Morrissey, Michael P., Sellers, William R., Schlegel, Robert, and Garraway, Levi A.

Published
2012
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49. Initial genome sequencing and analysis of multiple myeloma

Author

Chapman, Michael A., Lawrence, Michael S., Keats, Jonathan J., Cibulskis, Kristian, Sougnez, Carrie, Schinzel, Anna C., Harview, Christina L., Brunet, Jean-Philippe, Ahmann, Gregory J., Adli, Mazhar, Anderson, Kenneth C., Ardlie, Kristin G., Auclair, Daniel, Baker, Angela, Bergsagel, Leif P., Bernstein, Bradley E., Drier, Yotam, Fonseca, Rafael, Gabriel, Stacey B., Hofmeister, Craig C., Jagannath, Sundar, Jakubowiak, Andrzej J., Krishnan, Amrita, Levy, Joan, Liefeld, Ted, Lonial, Sagar, Mahan, Scott, Mfuko, Bunmi, Monti, Stefano, Perkins, Louise M., Onofrio, Robb, Pugh, Trevor J., Rajkumar, Vincent S., Ramos, Alex H., Siegel, David S., Sivachenko, Andrey, Stewart, Keith A., Trudel, Suzanne, Vij, Ravi, Voet, Douglas, Winckler, Wendy, Zimmerman, Todd, Carpten, John, Trent, Jeff, Hahn, William C., Garraway, Levi A., Meyerson, Matthew, Lander, Eric S., Getz, Gad, and Golub, Todd R.

Published
2011
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50. The genomic complexity of primary human prostate cancer

Author

Berger, Michael F., Lawrence, Michael S., Demichelis, Francesca, Drier, Yotam, Cibulskis, Kristian, Sivachenko, Andrey Y., Sboner, Andrea, Esgueva, Raquel, Pflueger, Dorothee, Sougnez, Carrie, Onofrio, Robert, Carter, Scott L., Park, Kyung, Habegger, Lukas, Ambrogio, Lauren, Fennell, Timothy, Parkin, Melissa, Saksena, Gordon, Voet, Douglas, Ramos, Alex H., Pugh, Trevor J., Wilkinson, Jane, Fisher, Sheila, Winckler, Wendy, Mahan, Scott, Ardlie, Kristin, Baldwin, Jennifer, Simons, Jonathan W., Kitabayashi, Naoki, MacDonald, Theresa Y., Kantoff, Philip W., Chin, Lynda, Gabriel, Stacey B., Gerstein, Mark B., Golub, Todd R., Meyerson, Matthew, Tewari, Ashutosh, Lander, Eric S., Getz, Gad, Rubin, Mark A., and Garraway, Levi A.

Published
2011
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