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1. Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma

Author

Ally, Adrian, Balasundaram, Miruna, Carlsen, Rebecca, Chuah, Eric, Clarke, Amanda, Dhalla, Noreen, Holt, Robert A, Jones, Steven JM, Lee, Darlene, Ma, Yussanne, Marra, Marco A, Mayo, Michael, Moore, Richard A, Mungall, Andrew J, Schein, Jacqueline E, Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Cheung, Dorothy, Wong, Tina, Brooks, Denise, Robertson, A Gordon, Bowlby, Reanne, Mungall, Karen, Sadeghi, Sara, Xi, Liu, Covington, Kyle, Shinbrot, Eve, Wheeler, David A, Gibbs, Richard A, Donehower, Lawrence A, Wang, Linghua, Bowen, Jay, Gastier-Foster, Julie M, Gerken, Mark, Helsel, Carmen, Leraas, Kristen M, Lichtenberg, Tara M, Ramirez, Nilsa C, Wise, Lisa, Zmuda, Erik, Gabriel, Stacey B, Meyerson, Matthew, Cibulskis, Carrie, Murray, Bradley A, Shih, Juliann, Beroukhim, Rameen, Cherniack, Andrew D, Schumacher, Steven E, Saksena, Gordon, Pedamallu, Chandra Sekhar, Chin, Lynda, Getz, Gad, Noble, Michael, Zhang, Hailei, Heiman, David, Cho, Juok, Gehlenborg, Nils, Voet, Douglas, Lin, Pei, Frazer, Scott, Defreitas, Timothy, Meier, Sam, Lawrence, Michael, Kim, Jaegil, Creighton, Chad J, Muzny, Donna, Doddapaneni, HarshaVardhan, Hu, Jianhong, Wang, Min, Morton, Donna, Korchina, Viktoriya, Han, Yi, Dinh, Huyen, Lewis, Lora, Bellair, Michelle, Liu, Xiuping, Santibanez, Jireh, Glenn, Robert, Lee, Sandra, Hale, Walker, Parker, Joel S, Wilkerson, Matthew D, Hayes, D Neil, Reynolds, Sheila M, Shmulevich, Ilya, Zhang, Wei, Liu, Yuexin, Iype, Lisa, Makhlouf, Hala, Torbenson, Michael S, Kakar, Sanjay, Yeh, Matthew M, Jain, Dhanpat, Kleiner, David E, Dhanasekaran, Renumathy, El-Serag, Hashem B, and Yim, Sun Young

Subjects
Human Genome, Digestive Diseases, Biotechnology, Rare Diseases, Genetics, Liver Disease, Liver Cancer, Cancer, Aetiology, 2.1 Biological and endogenous factors, 4.1 Discovery and preclinical testing of markers and technologies, Detection, screening and diagnosis, Good Health and Well Being, Carcinoma, Hepatocellular, DNA Methylation, Genomics, Humans, Isocitrate Dehydrogenase, Liver Neoplasms, MicroRNAs, Mutation, Cancer Genome Atlas Research Network. Electronic address: wheeler@bcm.edu, Cancer Genome Atlas Research Network, IDH1/2, TP53, cancer subtyping, expression profile, hepatocellular carcinoma, metabolic reprogramming, promoter hypermethylation, significantly mutated genes, sonic hedgehog signaling, stem cell phenotype, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Liver cancer has the second highest worldwide cancer mortality rate and has limited therapeutic options. We analyzed 363 hepatocellular carcinoma (HCC) cases by whole-exome sequencing and DNA copy number analyses, and we analyzed 196 HCC cases by DNA methylation, RNA, miRNA, and proteomic expression also. DNA sequencing and mutation analysis identified significantly mutated genes, including LZTR1, EEF1A1, SF3B1, and SMARCA4. Significant alterations by mutation or downregulation by hypermethylation in genes likely to result in HCC metabolic reprogramming (ALB, APOB, and CPS1) were observed. Integrative molecular HCC subtyping incorporating unsupervised clustering of five data platforms identified three subtypes, one of which was associated with poorer prognosis in three HCC cohorts. Integrated analyses enabled development of a p53 target gene expression signature correlating with poor survival. Potential therapeutic targets for which inhibitors exist include WNT signaling, MDM4, MET, VEGFA, MCL1, IDH1, TERT, and immune checkpoint proteins CTLA-4, PD-1, and PD-L1.

Published
2017

2. Integrated Molecular Characterization of Uterine Carcinosarcoma

Author

Cherniack, Andrew D, Shen, Hui, Walter, Vonn, Stewart, Chip, Murray, Bradley A, Bowlby, Reanne, Hu, Xin, Ling, Shiyun, Soslow, Robert A, Broaddus, Russell R, Zuna, Rosemary E, Robertson, Gordon, Laird, Peter W, Kucherlapati, Raju, Mills, Gordon B, Network, The Cancer Genome Atlas Research, Akbani, Rehan, Ally, Adrian, Auman, J Todd, Balasundaram, Miruna, Balu, Saianand, Baylin, Stephen B, Beroukhim, Rameen, Bodenheimer, Tom, Bogomolniy, Faina, Boice, Lori, Bootwalla, Moiz S, Bowen, Jay, Broaddus, Russell, Brooks, Denise, Carlsen, Rebecca, Cho, Juok, Chuah, Eric, Chudamani, Sudha, Cibulskis, Kristian, Cline, Melissa, Dao, Fanny, David, Mutch, Demchok, John A, Dhalla, Noreen, Dowdy, Sean, Felau, Ina, Ferguson, Martin L, Frazer, Scott, Frick, Jessica, Gabriel, Stacey, Gastier-Foster, Julie M, Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Gupta, Manaswi, Haussler, David, Hayes, D Neil, Heiman, David I, Hess, Julian, Hoadley, Katherine A, Hoffmann, Robert, Holt, Robert A, Hoyle, Alan P, Huang, Mei, Hutter, Carolyn M, Jefferys, Stuart R, Jones, Steven JM, Jones, Corbin D, Kanchi, Rupa S, Kandoth, Cyriac, Kasaian, Katayoon, Kerr, Sarah, Kim, Jaegil, Lai, Phillip H, Lander, Eric, Lawrence, Michael S, Lee, Darlene, Leraas, Kristen M, Leshchiner, Ignaty, Levine, Douglas A, Lichtenberg, Tara M, Lin, Pei, Liu, Jia, Liu, Wenbin, Liu, Yuexin, Lolla, Laxmi, Lu, Yiling, Ma, Yussanne, Maglinte, Dennis T, Marra, Marco A, Mayo, Michael, Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A, Moore, Richard A, Mose, Lisle E, Mungall, Andrew J, and Mungall, Karen

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Oncology and Carcinogenesis, Reproductive Medicine, Human Genome, Cancer, Biotechnology, 2.1 Biological and endogenous factors, Aetiology, Carcinosarcoma, DNA Copy Number Variations, Epithelial-Mesenchymal Transition, Female, Humans, Mutation, Uterine Neoplasms, Cancer Genome Atlas Research Network, EMT, TGGA, The Cancer Genome Atlas, UCS, endometrial cancer, epithelial-to-mesenchymal transition, gynecologic cancer, gynecologic oncology, translational science, uterine carcinosarcoma, Neurosciences, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

We performed genomic, epigenomic, transcriptomic, and proteomic characterizations of uterine carcinosarcomas (UCSs). Cohort samples had extensive copy-number alterations and highly recurrent somatic mutations. Frequent mutations were found in TP53, PTEN, PIK3CA, PPP2R1A, FBXW7, and KRAS, similar to endometrioid and serous uterine carcinomas. Transcriptome sequencing identified a strong epithelial-to-mesenchymal transition (EMT) gene signature in a subset of cases that was attributable to epigenetic alterations at microRNA promoters. The range of EMT scores in UCS was the largest among all tumor types studied via The Cancer Genome Atlas. UCSs shared proteomic features with gynecologic carcinomas and sarcomas with intermediate EMT features. Multiple somatic mutations and copy-number alterations in genes that are therapeutic targets were identified.

Published
2017

3. Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma

Author

Fishbein, Lauren, Leshchiner, Ignaty, Walter, Vonn, Danilova, Ludmila, Robertson, A Gordon, Johnson, Amy R, Lichtenberg, Tara M, Murray, Bradley A, Ghayee, Hans K, Else, Tobias, Ling, Shiyun, Jefferys, Stuart R, de Cubas, Aguirre A, Wenz, Brandon, Korpershoek, Esther, Amelio, Antonio L, Makowski, Liza, Rathmell, W Kimryn, Gimenez-Roqueplo, Anne-Paule, Giordano, Thomas J, L., Sylvia, Tischler, Arthur S, Network, The Cancer Genome Atlas Research, Akbani, Rehan, Ally, Adrian, Amar, Laurence, Arachchi, Harindra, Auchus, Richard J, Auman, J Todd, Baertsch, Robert, Balasundaram, Miruna, Balu, Saianand, Bartsch, Detlef K, Baudin, Eric, Bauer, Thomas, Beaver, Allison, Benz, Christopher, Beroukhim, Rameen, Beuschlein, Felix, Bodenheimer, Tom, Boice, Lori, Bowen, Jay, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Carter, Suzie, Cassol, Clarissa A, Cherniack, Andrew D, Chin, Lynda, Cho, Juok, Chuah, Eric, Chudamani, Sudha, Cope, Leslie, Crain, Daniel, Curley, Erin, de Krijger, Ronald R, Demchok, John A, Deutschbein, Timo, Dhalla, Noreen, Dimmock, David, Dinjens, Winand NM, Eng, Charis, Eschbacher, Jennifer, Fassnacht, Martin, Felau, Ina, Feldman, Michael, Ferguson, Martin L, Fiddes, Ian, Frazer, Scott, Gabriel, Stacey B, Gardner, Johanna, Gastier-Foster, Julie M, Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Geurts, Jennifer, Goldman, Mary, Graim, Kiley, Gupta, Manaswi, Haan, David, Hahner, Stefanie, Hantel, Constanze, Haussler, David, Hayes, D Neil, Heiman, David I, Hoadley, Katherine A, Holt, Robert A, Hoyle, Alan P, Huang, Mei, Hunt, Bryan, and Hutter, Carolyn M

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Neurosciences, Precision Medicine, Cancer, Human Genome, Cancer Genomics, Biotechnology, Rare Diseases, 2.1 Biological and endogenous factors, Aetiology, Good Health and Well Being, Adult, Aged, Aged, 80 and over, DNA-Binding Proteins, Female, Gene Fusion, Humans, Male, Middle Aged, Mutation, Nuclear Proteins, Paraganglioma, Pheochromocytoma, Pol1 Transcription Initiation Complex Proteins, Proto-Oncogene Proteins c-ret, RNA-Binding Proteins, Trans-Activators, Transcription Factors, Cancer Genome Atlas Research Network, CSDE1, MAML3, TCGA, expression subtypes, genomics, metastasis, molecular profiling, paraganglioma, pheochromocytoma, sequencing, Oncology and Carcinogenesis, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

We report a comprehensive molecular characterization of pheochromocytomas and paragangliomas (PCCs/PGLs), a rare tumor type. Multi-platform integration revealed that PCCs/PGLs are driven by diverse alterations affecting multiple genes and pathways. Pathogenic germline mutations occurred in eight PCC/PGL susceptibility genes. We identified CSDE1 as a somatically mutated driver gene, complementing four known drivers (HRAS, RET, EPAS1, and NF1). We also discovered fusion genes in PCCs/PGLs, involving MAML3, BRAF, NGFR, and NF1. Integrated analysis classified PCCs/PGLs into four molecularly defined groups: a kinase signaling subtype, a pseudohypoxia subtype, a Wnt-altered subtype, driven by MAML3 and CSDE1, and a cortical admixture subtype. Correlates of metastatic PCCs/PGLs included the MAML3 fusion gene. This integrated molecular characterization provides a comprehensive foundation for developing PCC/PGL precision medicine.

Published
2017

4. Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

Author

Zheng, Siyuan, Cherniack, Andrew D, Dewal, Ninad, Moffitt, Richard A, Danilova, Ludmila, Murray, Bradley A, Lerario, Antonio M, Else, Tobias, Knijnenburg, Theo A, Ciriello, Giovanni, Kim, Seungchan, Assie, Guillaume, Morozova, Olena, Akbani, Rehan, Shih, Juliann, Hoadley, Katherine A, Choueiri, Toni K, Waldmann, Jens, Mete, Ozgur, Robertson, A Gordon, Wu, Hsin-Ta, Raphael, Benjamin J, Shao, Lina, Meyerson, Matthew, Demeure, Michael J, Beuschlein, Felix, Gill, Anthony J, Sidhu, Stan B, Almeida, Madson Q, Fragoso, Maria CBV, Cope, Leslie M, Kebebew, Electron, Habra, Mouhammed A, Whitsett, Timothy G, Bussey, Kimberly J, Rainey, William E, L., Sylvia, Bertherat, Jérôme, Fassnacht, Martin, Wheeler, David A, Network, The Cancer Genome Atlas Research, Verhaak, Roel GW, Giordano, Thomas J, Hammer, Gary D, Assié, Guillaume, Wu, Hsin-Tu, Almeida, Madson, Fragoso, Maria Candida Barisson, Habra, Mouhammed Amir, Benz, Christopher, Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Butterfield, Yaron SN, Carlsen, Rebecca, Dhalla, Noreen, Guin, Ranabir, Holt, Robert A, Jones, Steven JM, Kasaian, Katayoon, Lee, Darlene, Li, Haiyan I, Lim, Lynette, Ma, Yussanne, and Marra, Marco A

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Human Genome, Cancer, Rare Diseases, Biotechnology, Clinical Research, Adolescent, Adrenal Cortex Neoplasms, Adrenocortical Carcinoma, Adult, Aged, Aged, 80 and over, Child, DNA Methylation, Disease-Free Survival, Female, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Genetic Predisposition to Disease, Genome, Human, Genomics, Humans, Male, Middle Aged, Mutation, Outcome Assessment, Health Care, Prognosis, Young Adult, Cancer Genome Atlas Research Network, Neurosciences, Oncology and Carcinogenesis, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

We describe a comprehensive genomic characterization of adrenocortical carcinoma (ACC). Using this dataset, we expand the catalogue of known ACC driver genes to include PRKAR1A, RPL22, TERF2, CCNE1, and NF1. Genome wide DNA copy-number analysis revealed frequent occurrence of massive DNA loss followed by whole-genome doubling (WGD), which was associated with aggressive clinical course, suggesting WGD is a hallmark of disease progression. Corroborating this hypothesis were increased TERT expression, decreased telomere length, and activation of cell-cycle programs. Integrated subtype analysis identified three ACC subtypes with distinct clinical outcome and molecular alterations which could be captured by a 68-CpG probe DNA-methylation signature, proposing a strategy for clinical stratification of patients based on molecular markers.

Published
2016

5. Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma

Author

Linehan, W Marston, Spellman, Paul T, Ricketts, Christopher J, Creighton, Chad J, Fei, Suzanne S, Davis, Caleb, Wheeler, David A, Murray, Bradley A, Schmidt, Laura, Vocke, Cathy D, Peto, Myron, Al Mamun, Abu Amar M, Shinbrot, Eve, Sethi, Anurag, Brooks, Samira, Rathmell, W Kimryn, Brooks, Angela N, Hoadley, Katherine A, Robertson, A Gordon, Brooks, Denise, Bowlby, Reanne, Sadeghi, Sara, Shen, Hui, Weisenberger, Daniel J, Bootwalla, Moiz, Baylin, Stephen B, Laird, Peter W, Cherniack, Andrew D, Saksena, Gordon, Haake, Scott, Li, Jun, Liang, Han, Lu, Yiling, Mills, Gordon B, Akbani, Rehan, Leiserson, Mark DM, Raphael, Benjamin J, Anur, Pavana, Bottaro, Donald, Albiges, Laurence, Barnabas, Nandita, Choueiri, Toni K, Czerniak, Bogdan, Godwin, Andrew K, Hakimi, A Ari, Ho, Thai H, Hsieh, James, Ittmann, Michael, Kim, William Y, Krishnan, Bhavani, Merino, Maria J, Mills Shaw, Kenna R, Reuter, Victor E, Reznik, Ed, Shelley, Carl S, Shuch, Brian, Signoretti, Sabina, Srinivasan, Ramaprasad, Tamboli, Pheroze, Thomas, George, Tickoo, Satish, Burnett, Kenneth, Crain, Daniel, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph D, Penny, Robert J, Shelton, Candace, Shelton, W Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Avedon, Melissa T, Bowen, Jay, Gastier-Foster, Julie M, Gerken, Mark, Leraas, Kristen M, Lichtenberg, Tara M, Ramirez, Nilsa C, Santos, Tracie, Wise, Lisa, Zmuda, Erik, Demchok, John A, Felau, Ina, Hutter, Carolyn M, Sheth, Margi, Sofia, Heidi J, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C, Zhang, Jiashan, Ayala, Brenda, Baboud, Julien, Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, and Naresh, Rashi

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Cancer, Rare Diseases, Genetics, Biotechnology, Digestive Diseases, Kidney Disease, Good Health and Well Being, Carcinoma, Papillary, CpG Islands, DNA Methylation, Humans, Kidney Neoplasms, MicroRNAs, Mutation, NF-E2-Related Factor 2, Phenotype, Proto-Oncogene Proteins c-met, RNA, Messenger, RNA, Neoplasm, Sequence Analysis, RNA, Signal Transduction, Cancer Genome Atlas Research Network, Medical and Health Sciences, General & Internal Medicine, Biomedical and clinical sciences, Health sciences
Abstract

BackgroundPapillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist.MethodsWe performed comprehensive molecular characterization of 161 primary papillary renal-cell carcinomas, using whole-exome sequencing, copy-number analysis, messenger RNA and microRNA sequencing, DNA-methylation analysis, and proteomic analysis.ResultsType 1 and type 2 papillary renal-cell carcinomas were shown to be different types of renal cancer characterized by specific genetic alterations, with type 2 further classified into three individual subgroups on the basis of molecular differences associated with patient survival. Type 1 tumors were associated with MET alterations, whereas type 2 tumors were characterized by CDKN2A silencing, SETD2 mutations, TFE3 fusions, and increased expression of the NRF2-antioxidant response element (ARE) pathway. A CpG island methylator phenotype (CIMP) was observed in a distinct subgroup of type 2 papillary renal-cell carcinomas that was characterized by poor survival and mutation of the gene encoding fumarate hydratase (FH).ConclusionsType 1 and type 2 papillary renal-cell carcinomas were shown to be clinically and biologically distinct. Alterations in the MET pathway were associated with type 1, and activation of the NRF2-ARE pathway was associated with type 2; CDKN2A loss and CIMP in type 2 conveyed a poor prognosis. Furthermore, type 2 papillary renal-cell carcinoma consisted of at least three subtypes based on molecular and phenotypic features. (Funded by the National Institutes of Health.).

Published
2016

6. Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

Author

Ceccarelli, Michele, Barthel, Floris P, Malta, Tathiane M, Sabedot, Thais S, Salama, Sofie R, Murray, Bradley A, Morozova, Olena, Newton, Yulia, Radenbaugh, Amie, Pagnotta, Stefano M, Anjum, Samreen, Wang, Jiguang, Manyam, Ganiraju, Zoppoli, Pietro, Ling, Shiyun, Rao, Arjun A, Grifford, Mia, Cherniack, Andrew D, Zhang, Hailei, Poisson, Laila, Carlotti, Carlos Gilberto, da Cunha Tirapelli, Daniela Pretti, Rao, Arvind, Mikkelsen, Tom, Lau, Ching C, Yung, WK Alfred, Rabadan, Raul, Huse, Jason, Brat, Daniel J, Lehman, Norman L, Barnholtz-Sloan, Jill S, Zheng, Siyuan, Hess, Kenneth, Rao, Ganesh, Meyerson, Matthew, Beroukhim, Rameen, Cooper, Lee, Akbani, Rehan, Wrensch, Margaret, Haussler, David, Aldape, Kenneth D, Laird, Peter W, Gutmann, David H, Network, TCGA Research, Arachchi, Harindra, Auman, J Todd, Balasundaram, Miruna, Balu, Saianand, Barnett, Gene, Baylin, Stephen, Bell, Sue, Benz, Christopher, Bir, Natalie, Black, Keith L, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S, Bowen, Jay, Bristow, Christopher A, Butterfield, Yaron SN, Chen, Qing-Rong, Chin, Lynda, Cho, Juok, Chuah, Eric, Chudamani, Sudha, Coetzee, Simon G, Cohen, Mark L, Colman, Howard, Couce, Marta, D’Angelo, Fulvio, Davidsen, Tanja, Davis, Amy, Demchok, John A, Devine, Karen, Ding, Li, Duell, Rebecca, Elder, J Bradley, Eschbacher, Jennifer M, Fehrenbach, Ashley, Ferguson, Martin, Frazer, Scott, Fuller, Gregory, Fulop, Jordonna, Gabriel, Stacey B, Garofano, Luciano, Gastier-Foster, Julie M, Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Giannini, Caterina, Gibson, William J, Hadjipanayis, Angela, Hayes, D Neil, Heiman, David I, Hermes, Beth, Hilty, Joe, Hoadley, Katherine A, Hoyle, Alan P, and Huang, Mei

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Bioinformatics and Computational Biology, Genetics, Oncology and Carcinogenesis, Orphan Drug, Brain Cancer, Brain Disorders, Biotechnology, Human Genome, Rare Diseases, Neurosciences, Cancer, Adult, Brain Neoplasms, Cell Proliferation, Cluster Analysis, DNA Helicases, DNA Methylation, Epigenesis, Genetic, Glioma, Humans, Isocitrate Dehydrogenase, Middle Aged, Mutation, Nuclear Proteins, Promoter Regions, Genetic, Signal Transduction, Telomerase, Telomere, Transcriptome, X-linked Nuclear Protein, TCGA Research Network, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

Therapy development for adult diffuse glioma is hindered by incomplete knowledge of somatic glioma driving alterations and suboptimal disease classification. We defined the complete set of genes associated with 1,122 diffuse grade II-III-IV gliomas from The Cancer Genome Atlas and used molecular profiles to improve disease classification, identify molecular correlations, and provide insights into the progression from low- to high-grade disease. Whole-genome sequencing data analysis determined that ATRX but not TERT promoter mutations are associated with increased telomere length. Recent advances in glioma classification based on IDH mutation and 1p/19q co-deletion status were recapitulated through analysis of DNA methylation profiles, which identified clinically relevant molecular subsets. A subtype of IDH mutant glioma was associated with DNA demethylation and poor outcome; a group of IDH-wild-type diffuse glioma showed molecular similarity to pilocytic astrocytoma and relatively favorable survival. Understanding of cohesive disease groups may aid improved clinical outcomes.

Published
2016

7. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

Author

Brat, Daniel J, Verhaak, Roel GW, Aldape, Kenneth D, Yung, WK Alfred, Salama, Sofie R, Cooper, Lee AD, Rheinbay, Esther, Miller, C Ryan, Vitucci, Mark, Morozova, Olena, Robertson, A Gordon, Noushmehr, Houtan, Laird, Peter W, Cherniack, Andrew D, Akbani, Rehan, Huse, Jason T, Ciriello, Giovanni, Poisson, Laila M, Barnholtz-Sloan, Jill S, Berger, Mitchel S, Brennan, Cameron, Colen, Rivka R, Colman, Howard, Flanders, Adam E, Giannini, Caterina, Grifford, Mia, Iavarone, Antonio, Jain, Rajan, Joseph, Isaac, Kim, Jaegil, Kasaian, Katayoon, Mikkelsen, Tom, Murray, Bradley A, O'Neill, Brian Patrick, Pachter, Lior, Parsons, Donald W, Sougnez, Carrie, Sulman, Erik P, Vandenberg, Scott R, Van Meir, Erwin G, von Deimling, Andreas, Zhang, Hailei, Crain, Daniel, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Troy, Sherman, Mark, Yena, Peggy, Black, Aaron, Bowen, Jay, Dicostanzo, Katie, Gastier-Foster, Julie, Leraas, Kristen M, Lichtenberg, Tara M, Pierson, Christopher R, Ramirez, Nilsa C, Taylor, Cynthia, Weaver, Stephanie, Wise, Lisa, Zmuda, Erik, Davidsen, Tanja, Demchok, John A, Eley, Greg, Ferguson, Martin L, Hutter, Carolyn M, Mills Shaw, Kenna R, Ozenberger, Bradley A, Sheth, Margi, Sofia, Heidi J, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean Claude, Ayala, Brenda, Baboud, Julien, Chudamani, Sudha, Jensen, Mark A, Liu, Jia, Pihl, Todd, Raman, Rohini, Wan, Yunhu, Wu, Ye, Ally, Adrian, Auman, J Todd, Balasundaram, Miruna, Balu, Saianand, Baylin, Stephen B, Beroukhim, Rameen, Bootwalla, Moiz S, Bowlby, Reanne, Bristow, Christopher A, Brooks, Denise, Butterfield, Yaron, Carlsen, Rebecca, Carter, Scott, Chin, Lynda, and Chu, Andy

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Clinical Research, Human Genome, Brain Cancer, Rare Diseases, Neurosciences, Biotechnology, Cancer Genomics, Genetics, Cancer, Brain Disorders, Adolescent, Adult, Aged, Chromosomes, Human, Pair 1, Chromosomes, Human, Pair 19, Cluster Analysis, DNA, Neoplasm, Female, Genes, p53, Glioblastoma, Glioma, Humans, Kaplan-Meier Estimate, Male, Middle Aged, Mutation, Neoplasm Grading, Proportional Hazards Models, Sequence Analysis, DNA, Signal Transduction, Cancer Genome Atlas Research Network, Medical and Health Sciences, General & Internal Medicine, Biomedical and clinical sciences, Health sciences
Abstract

BackgroundDiffuse low-grade and intermediate-grade gliomas (which together make up the lower-grade gliomas, World Health Organization grades II and III) have highly variable clinical behavior that is not adequately predicted on the basis of histologic class. Some are indolent; others quickly progress to glioblastoma. The uncertainty is compounded by interobserver variability in histologic diagnosis. Mutations in IDH, TP53, and ATRX and codeletion of chromosome arms 1p and 19q (1p/19q codeletion) have been implicated as clinically relevant markers of lower-grade gliomas.MethodsWe performed genomewide analyses of 293 lower-grade gliomas from adults, incorporating exome sequence, DNA copy number, DNA methylation, messenger RNA expression, microRNA expression, and targeted protein expression. These data were integrated and tested for correlation with clinical outcomes.ResultsUnsupervised clustering of mutations and data from RNA, DNA-copy-number, and DNA-methylation platforms uncovered concordant classification of three robust, nonoverlapping, prognostically significant subtypes of lower-grade glioma that were captured more accurately by IDH, 1p/19q, and TP53 status than by histologic class. Patients who had lower-grade gliomas with an IDH mutation and 1p/19q codeletion had the most favorable clinical outcomes. Their gliomas harbored mutations in CIC, FUBP1, NOTCH1, and the TERT promoter. Nearly all lower-grade gliomas with IDH mutations and no 1p/19q codeletion had mutations in TP53 (94%) and ATRX inactivation (86%). The large majority of lower-grade gliomas without an IDH mutation had genomic aberrations and clinical behavior strikingly similar to those found in primary glioblastoma.ConclusionsThe integration of genomewide data from multiple platforms delineated three molecular classes of lower-grade gliomas that were more concordant with IDH, 1p/19q, and TP53 status than with histologic class. Lower-grade gliomas with an IDH mutation either had 1p/19q codeletion or carried a TP53 mutation. Most lower-grade gliomas without an IDH mutation were molecularly and clinically similar to glioblastoma. (Funded by the National Institutes of Health.).

Published
2015

8. The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma

Author

Davis, Caleb F, Ricketts, Christopher J, Wang, Min, Yang, Lixing, Cherniack, Andrew D, Shen, Hui, Buhay, Christian, Kang, Hyojin, Kim, Sang Cheol, Fahey, Catherine C, Hacker, Kathryn E, Bhanot, Gyan, Gordenin, Dmitry A, Chu, Andy, Gunaratne, Preethi H, Biehl, Michael, Seth, Sahil, Kaipparettu, Benny A, Bristow, Christopher A, Donehower, Lawrence A, Wallen, Eric M, Smith, Angela B, Tickoo, Satish K, Tamboli, Pheroze, Reuter, Victor, Schmidt, Laura S, Hsieh, James J, Choueiri, Toni K, Hakimi, A Ari, Network, The Cancer Genome Atlas Research, Creighton, Chad J, Morgan, Margaret, Wheeler, David A, Gibbs, Richard A, Signoretti, Sabina, Robertson, A Gordon, Henske, Elizabeth P, Kwiatkowski, David J, Ricketts, Christopher, Linehan, W Marston, Seiler, Michael, Rathmell, W Kimryn, Laird, Peter W, Shuch, Brian, Muzny, Donna, Chao, Hsu, Dahdouli, Mike, Xi, Liu, Kakkar, Nipun, Reid, Jeffrey G, Downs, Brittany, Drummond, Jennifer, Morton, Donna, Doddapaneni, Harsha, Lewis, Lora, English, Adam, Meng, Qingchang, Kovar, Christie, Wang, Qiaoyan, Hale, Walker, Hawes, Alicia, Kalra, Divya, Walker, Kimberly, Murray, Bradley A, Sougnez, Carrie, Saksena, Gordon, Carter, Scott L, Schumacher, Steven E, Tabak, Barbara, Zack, Travis I, Getz, Gad, Beroukhim, Rameen, Gabriel, Stacey B, Meyerson, Matthew, Ally, Adrian, Balasundaram, Miruna, Birol, Inanc, and Brooks, Denise

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Bioinformatics and Computational Biology, Genetics, Oncology and Carcinogenesis, Biotechnology, Rare Diseases, Kidney Disease, Cancer, Cancer Genomics, Human Genome, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, Base Sequence, Carcinoma, Renal Cell, Chromosome Breakpoints, Chromosome Deletion, Chromosomes, Human, DNA Copy Number Variations, DNA Methylation, DNA Mutational Analysis, DNA, Mitochondrial, Exome, Genome, Human, Humans, Kidney Neoplasms, Molecular Sequence Data, Promoter Regions, Genetic, Telomerase, Transcriptome, The Cancer Genome Atlas Research Network, Neurosciences, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

We describe the landscape of somatic genomic alterations of 66 chromophobe renal cell carcinomas (ChRCCs) on the basis of multidimensional and comprehensive characterization, including mtDNA and whole-genome sequencing. The result is consistent that ChRCC originates from the distal nephron compared with other kidney cancers with more proximal origins. Combined mtDNA and gene expression analysis implicates changes in mitochondrial function as a component of the disease biology, while suggesting alternative roles for mtDNA mutations in cancers relying on oxidative phosphorylation. Genomic rearrangements lead to recurrent structural breakpoints within TERT promoter region, which correlates with highly elevated TERT expression and manifestation of kataegis, representing a mechanism of TERT upregulation in cancer distinct from previously observed amplifications and point mutations.

Published
2014

9. Artifactuality

Author

Murray, Bradley

Subjects
100
Published
2008

12. Integrated genomic and molecular characterization of cervical cancer

Author

Burk, Robert D., Chen, Zigui, Saller, Charles, Tarvin, Katherine, Carvalho, Andre L., Scapulatempo-Neto, Cristovam, Silveira, Henrique C., Fregnani, Jos H., Creighton, Chad J., Anderson, Matthew L., Castro, Patricia, Wang, Sophia S., Yau, Christina, Benz, Christopher, Robertson, A. Gordon, Mungall, Karen, Lim, Lynette, Bowlby, Reanne, Sadeghi, Sara, Brooks, Denise, Sipahimalani, Payal, Mar, Richard, Ally, Adrian, Clarke, Amanda, Mungall, Andrew J., Tam, Angela, Lee, Darlene, Chuah, Eric, Schein, Jacqueline E., Tse, Kane, Kasaian, Katayoon, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Balasundaram, Miruna, Thiessen, Nina, Dhalla, Noreen, Carlsen, Rebecca, Moore, Richard A., Holt, Robert A., Jones, Steven J. M., Wong, Tina, Pantazi, Angeliki, Parfenov, Michael, Kucherlapati, Raju, Hadjipanayis, Angela, Seidman, Jonathan, Kucherlapati, Melanie, Ren, Xiaojia, Xu, Andrew W., Yang, Lixing, Park, Peter J., Lee, Semin, Rabeno, Brenda, Huelsenbeck-Dill, Lori, Borowsky, Mark, Cadungog, Mark, Iacocca, Mary, Petrelli, Nicholas, Swanson, Patricia, Ojesina, Akinyemi I., Le, Xuan, Sandusky, George, Adebamowo, Sally N., Akeredolu, Teniola, Adebamowo, Clement, Reynolds, Sheila M., Shmulevich, Ilya, Shelton, Candace, Crain, Daniel, Mallery, David, Curley, Erin, Gardner, Johanna, Penny, Robert, Morris, Scott, Shelton, Troy, Liu, Jia, Lolla, Laxmi, Chudamani, Sudha, Wu, Ye, Birrer, Michael, McLellan, Michael D., Bailey, Matthew H., Miller, Christopher A., Wyczalkowski, Matthew A., Fulton, Robert S., Fronick, Catrina C., Lu, Charles, Mardis, Elaine R., Appelbaum, Elizabeth L., Schmidt, Heather K., Fulton, Lucinda A., Cordes, Matthew G., Li, Tiandao, Ding, Li, Wilson, Richard K., Rader, Janet S., Behmaram, Behnaz, Uyar, Denise, Bradley, William, Wrangle, John, Pastore, Alessandro, Levine, Douglas A., Dao, Fanny, Gao, Jianjiong, Schultz, Nikolaus, Sander, Chris, Ladanyi, Marc, Einstein, Mark, Teeter, Randall, Benz, Stephen, Wentzensen, Nicolas, Felau, Ina, Zenklusen, Jean C., Bodelon, Clara, Demchok, John A., Yang, Liming, Sheth, Margi, Ferguson, Martin L., Tarnuzzer, Roy, Yang, Hannah, Schiffman, Mark, Zhang, Jiashan, Wang, Zhining, Davidsen, Tanja, Olaniyan, Olayinka, Hutter, Carolyn M., Sofia, Heidi J., Gordenin, Dmitry A., Chan, Kin, Roberts, Steven A., Klimczak, Leszek J., Van Waes, Carter, Chen, Zhong, Saleh, Anthony D., Cheng, Hui, Parfitt, Jeremy, Bartlett, John, Albert, Monique, Arnaout, Angel, Sekhon, Harman, Gilbert, Sebastien, Peto, Myron, Myers, Jerome, Harr, Jodi, Eckman, John, Bergsten, Julie, Tucker, Kelinda, Zach, Leigh Anne, Karlan, Beth Y., Lester, Jenny, Orsulic, Sandra, Sun, Qiang, Naresh, Rashi, Pihl, Todd, Wan, Yunhu, Zaren, Howard, Sapp, Jennifer, Miller, Judy, Drwiega, Paul, Murray, Bradley A., Zhang, Hailei, Cherniack, Andrew D., Sougnez, Carrie, Pedamallu, Chandra Sekhar, Lichtenstein, Lee, Meyerson, Matthew, Noble, Michael S., Heiman, David I., Voet, Doug, Getz, Gad, Saksena, Gordon, Kim, Jaegil, Shih, Juliann, Cho, Juok, Lawrence, Michael S., Gehlenborg, Nils, Lin, Pei, Beroukhim, Rameen, Frazer, Scott, Gabriel, Stacey B., Schumacher, Steven E., Leraas, Kristen M., Lichtenberg, Tara M., Zmuda, Erik, Bowen, Jay, Frick, Jessica, Gastier-Foster, Julie M., Wise, Lisa, Gerken, Mark, Ramirez, Nilsa C., Danilova, Ludmila, Cope, Leslie, Baylin, Stephen B., Salvesen, Helga B., Vellano, Christopher P., Ju, Zhenlin, Diao, Lixia, Zhao, Hao, Chong, Zechen, Ryan, Michael C., Martinez-Ledesma, Emmanuel, Verhaak, Roeland G., Averett Byers, Lauren, Yuan, Yuan, Chen, Ken, Ling, Shiyun, Mills, Gordon B., Lu, Yiling, Akbani, Rehan, Seth, Sahil, Liang, Han, Wang, Jing, Han, Leng, Weinstein, John N., Bristow, Christopher A., Zhang, Wei, Mahadeshwar, Harshad S., Sun, Huandong, Tang, Jiabin, Zhang, Jianhua, Song, Xingzhi, Protopopov, Alexei, Shaw, Kenna R. Mills, Chin, Lynda, Olabode, Oluwole, DiSaia, Philip, Radenbaugh, Amie, Haussler, David, Zhu, Jingchun, Stuart, Josh, Chalise, Prabhakar, Koestler, Devin, Fridley, Brooke L., Godwin, Andrew K., Madan, Rashna, Ciriello, Giovanni, Martinez, Cathleen, Higgins, Kelly, Bocklage, Therese, Auman, J. Todd, Perou, Charles M., Tan, Donghui, Parker, Joel S., Hoadley, Katherine A., Wilkerson, Matthew D., Mieczkowski, Piotr A., Skelly, Tara, Veluvolu, Umadevi, Hayes, D. Neil, Rathmell, W. Kimryn, Hoyle, Alan P., Simons, Janae V., Wu, Junyuan, Mose, Lisle E., Soloway, Matthew G., Balu, Saianand, Meng, Shaowu, Jefferys, Stuart R., Bodenheimer, Tom, Shi, Yan, Roach, Jeffrey, Thorne, Leigh B., Boice, Lori, Huang, Mei, Jones, Corbin D., Zuna, Rosemary, Walker, Joan, Gunderson, Camille, Snowbarger, Carie, Brown, David, Moxley, Katherine, Moore, Kathleen, Andrade, Kelsi, Landrum, Lisa, Mannel, Robert, McMeekin, Scott, Johnson, Starla, Nelson, Tina, Elishaev, Esther, Dhir, Rajiv, Edwards, Robert, Bhargava, Rohit, Tiezzi, Daniel G., Andrade, Jurandyr M., Noushmehr, Houtan, Gilberto Carlotti, Carlos, Jr, Tirapelli, Daniela Pretti da Cunha, Weisenberger, Daniel J., Van Den Berg, David J., Maglinte, Dennis T., Bootwalla, Moiz S., Lai, Phillip H., Triche, Timothy, Jr, Swisher, Elizabeth M., Agnew, Kathy J., Shelley, Carl Simon, Laird, Peter W., Schwarz, Julie, Grigsby, Perry, and Mutch, David

Subjects
Cervical cancer -- Genetic aspects -- Care and treatment -- Causes of, Gene mutation -- Health aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Cervical cancer remains one of the leading causes of cancer-related deaths worldwide. Here we report the extensive molecular characterization of 228 primary cervical cancers, one of the largest comprehensive genomic studies of cervical cancer to date. We observed notable APOBEC mutagenesis patterns and identified SHKBP1, ERBB3, CASP8, HLA-A and TGFBR2 as novel significantly mutated genes in cervical cancer. We also discovered amplifications in immune targets CD274 (also known as PD-L1) and PDCD1LG2 (also known as PD-L2), and the BCAR4 long non-coding RNA, which has been associated with response to lapatinib. Integration of human papilloma virus (HPV) was observed in all HPV18-related samples and 76% of HPV16-related samples, and was associated with structural aberrations and increased target-gene expression. We identified a unique set of endometrial-like cervical cancers, comprised predominantly of HPV-negative tumours with relatively high frequencies of KRAS, ARID1A and PTEN mutations. Integrative clustering of 178 samples identified keratin-low squamous, keratin-high squamous and adenocarcinoma-rich subgroups. These molecular analyses reveal new potential therapeutic targets for cervical cancers., Author(s): The Cancer Genome Atlas Research Network; Albert Einstein College of Medicine; Robert D. Burk [1]; Zigui Chen [1]; Analytical Biological Services; Charles Saller [2]; Katherine Tarvin [2]; Barretos Cancer [...]

Published
2017
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14. Integrated genomic characterization of oesophageal carcinoma

Author

Kim, Jihun, Bowlby, Reanne, Mungall, Andrew J., Robertson, Gordon A., Odze, Robert D., Cherniack, Andrew D., Shih, Juliann, Pedamallu, Chandra Sekhar, Cibulskis, Carrie, Dunford, Andrew, Meier, Samuel R., Kim, Jaegil, Raphael, Benjamin J., Wu, Hsin-Ta, Wong, Alexandra M., Willis, Joseph E., Bass, Adam J., Derks, Sarah, Garman, Katherine, McCall, Shannon J., Wiznerowicz, Maciej, Pantazi, Angeliki, Parfenov, Michael, Thorsson, Vésteinn, Shmulevich, Ilya, Dhankani, Varsha, Miller, Michael, Sakai, Ryo, Wang, Kenneth, Schultz, Nikolaus, Shen, Ronglai, Arora, Arshi, Weinhold, Nils, Sánchez-Vega, Francisco, Kelsen, David P., Zhang, Julia, Felau, Ina, Demchok, John, Rabkin, Charles S., Camargo, Constanza M., Zenklusen, Jean Claude, Bowen, Jay, Leraas, Kristen, Lichtenberg, Tara M., Curtis, Christina, Seoane, Jose A., Ojesina, Akinyemi I., Beer, David G., Gulley, Margaret L., Pennathur, Arjun, Luketich, James D., Zhou, Zhongren, Weisenberger, Daniel J., Akbani, Rehan, Lee, Ju-Seog, Liu, Wenbin, Mills, Gordon B., Zhang, Wei, Reid, Brian J, Hinoue, Toshinori, Laird, Peter W., Shen, Hui, Piazuelo, Blanca M., Schneider, Barbara G., McLellan, Michael, Taylor-Weiner, Amaro, Cibulskis, Carrie, Lawrence, Michael, Cibulskis, Kristian, Stewart, Chip, Getz, Gad, Lander, Eric, Gabriel, Stacey B., Ding, Li, McLellan, Michael D., Miller, Christopher A., Appelbaum, Elizabeth L., Cordes, Matthew G., Fronick, Catrina C., Fulton, Lucinda A., Mardis, Elaine R., Wilson, Richard K., Schmidt, Heather K., Fulton, Robert S., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert A., Jones, Steven J. M., Kasaian, Katayoon, Brooks, Denise, Li, Haiyan I., Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen L., Robertson, Gordon A., Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Wong, Tina, Cherniack, Andrew D., Shih, Juliann, Pedamallu, Chandra Sekhar, Beroukhim, Rameen, Bullman, Susan, Cibulskis, Carrie, Murray, Bradley A., Saksena, Gordon, Schumacher, Steven E., Gabriel, Stacey, Meyerson, Matthew, Hadjipanayis, Angela, Kucherlapati, Raju, Pantazi, Angeliki, Parfenov, Michael, Ren, Xiaojia, Park, Peter J., Lee, Semin, Kucherlapati, Melanie, Yang, Lixing, Baylin, Stephen B., Hoadley, Katherine A., Weisenberger, Daniel J., Bootwalla, Moiz S., Lai, Phillip H., Van Den Berg, David J., Berrios, Mario, Holbrook, Andrea, Akbani, Rehan, Hwang, Jun-Eul, Jang, Hee-Jin, Liu, Wenbin, Weinstein, John N., Lee, Ju-Seog, Lu, Yiling, Sohn, Bo Hwa, Mills, Gordon, Seth, Sahil, Protopopov, Alexei, Bristow, Christopher A., Mahadeshwar, Harshad S., Tang, Jiabin, Song, Xingzhi, Zhang, Jianhua, Laird, Peter W., Hinoue, Toshinori, Shen, Hui, Cho, Juok, Defrietas, Timothy, Frazer, Scott, Gehlenborg, Nils, Heiman, David I., Lawrence, Michael S., Lin, Pei, Meier, Samuel R., Noble, Michael S., Voet, Doug, Zhang, Hailei, Kim, Jaegil, Polak, Paz, Saksena, Gordon, Chin, Lynda, Getz, Gad, Wong, Alexandra M., Raphael, Benjamin J., Wu, Hsin-Ta, Lee, Semin, Park, Peter J., Yang, Lixing, Thorsson, Vésteinn, Bernard, Brady, Iype, Lisa, Miller, Michael, Reynolds, Sheila M., Shmulevich, Ilya, Dhankani, Varsha, Abeshouse, Adam, Arora, Arshi, Armenia, Joshua, Kundra, Ritika, Ladanyi, Marc, Lehmann, Kjong-Van, Gao, Jianjiong, Sander, Chris, Schultz, Nikolaus, Sánchez-Vega, Francisco, Shen, Ronglai, Weinhold, Nils, Chakravarty, Debyani, Zhang, Hongxin, Radenbaugh, Amie, Hegde, Apruva, Akbani, Rehan, Liu, Wenbin, Weinstein, John N., Chin, Lynda, Bristow, Christopher A., Lu, Yiling, Penny, Robert, Crain, Daniel, Gardner, Johanna, Curley, Erin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Shelton, Troy, Shelton, Candace, Bowen, Jay, Frick, Jessica, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Tarvin, Katherine, Saller, Charles, Park, Young Soo, Button, Michael, Carvalho, Andre L., Reis, Rui Manuel, Matsushita, Marcus Medeiros, Lucchesi, Fabiano, de Oliveira, Antonio Talvane, Le, Xuan, Paklina, Oxana, Setdikova, Galiya, Lee, Jae-Hyuck, Bennett, Joseph, Iacocca, Mary, Huelsenbeck-Dill, Lori, Potapova, Olga, Voronina, Olga, Liu, Ouida, Fulidou, Victoria, Cates, Crystal, Sharp, Alexis, Behera, Madhusmitara, Force, Seth, Khuri, Fadio, Owonikoko, Taofeek, Pickens, Allan, Ramalingam, Suresh, Sica, Gabriel, Dinjens, Winand, van Nistelrooij, Anna, Wijnhoven, Bas, Sandusky, George, Stepa, Serghei, Crain, Daniel, Paulauskis, Joseph, Penny, Robert, Gardner, Johanna, Mallery, David, Morris, Scott, Shelton, Troy, Shelton, Candace, Curley, Erin, Juhl, Hartmut, Zornig, Carsten, Kwon, Sun Young, Kelsen, David, Kim, Hark Kyun, Bartlett, John, Parfitt, Jeremy, Chetty, Runjan, Darling, Gail, Knox, Jennifer, Wong, Rebecca, El-Zimaity, Haila, Liu, Geoffrey, Boussioutas, Alex, Park, Do Young, Kemp, Rafael, Carlotti, Carlos Gilberto, da Cunha Tirapelli, Daniela Pretti, Saggioro, Fabiano Pinto, Sankarankutty, Ajith Kumar, Noushmehr, Houtan, dos Santos, Jose Sebastião, Trevisan, Felipe Amstalden, Eschbacher, Jennifer, Dubina, Michael, Mozgovoy, Eugene, Carey, Frank, Chalmers, Sally, Forgie, Ian, Godwin, Andrew, Reilly, Colleen, Madan, Rashna, Naima, Zaid, Ferrer-Torres, Daysha, Vinco, Michele, Rathmell, Kimryn W., Dhir, Rajiv, Luketich, James, Pennathur, Arjun, Ajani, Jaffer A., McCall, Shannon J., Janjigian, Yelena, Kelsen, David, Ladanyi, Marc, Tang, Laura, Camargo, Constanza M., Ajani, Jaffer A., Cheong, Jae-Ho, Chudamani, Sudha, Liu, Jai, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Demchok, John A., Felau, Ina, Ferguson, Martin L., Shaw, Kenna R. Mills, Sheth, Margi, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean Claude, Hutter, Carolyn M., Sofia, Heidi J., and Zhang, Jiashan

Published
2017
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15. Supplement to: Comprehensive, integrative genomic analysis of diffuse lower-grade gliomas.

Author

Brat, Daniel J, Verhaak, Roel GW, Salama, Sofie R., Cooper, Lee, Aldape, Kenneth D, Yung, Alfred W.K, Akbani, Rehan, Barnholtz-Sloan, Jill S., Berger, Mitchel S., Brennan, Cameron, Bristow, Christopher A., Cherniack, Andrew D., Ciriello, Giovanni, Colen, Rivka, Colman, Howard, Flanders, Adam E., Giannini, Caterina, Grifford, Mia, Huse, Jason T., Iavarone, Antonio, Jain, Rajan, Joseph, Isaac, Kim, Jaegil, Kasaian, Katayoon, Laird, Peter W., Mikkelsen, Tom, Miller, Ryan C., Morozova, Olena, Murray, Bradley A., Noushmehr, Houtan, OʼNeill, Brian Patrick, Pachter, Lior, Parsons, Donald W., Poisson, Laila M., Rheinbay, Esther, Robertson, Gordon A., Sougnez, Carrie, Sulman, Erik P., Vandenberg, Scott R., Van Meir, Erwin G., Vitucci, Mark, Deimling, Andreas von, Yoshihara, Kosuke, Zhang, Hailei, Zheng, Siyuan, Crain, Daniel, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Troy, Sherman, Mark, Yena, Peggy, Black, Aaron, Bowen, Jay, Dicostanzo, Katie, Gastier-Foster, Julie, Leraas, Kristen M., Lichtenberg, Tara M., Pierson, Christopher R., Ramirez, Nilsa C., Taylor, Cynthia, Weaver, Stephanie, Wise, Lisa, Zmuda, Erik, Davidsen, Tanja, Demchok, John A., Eley, Greg, Ferguson, Martin L., Hutter, Carolyn M., Mills Shaw, Kenna R., Ozenberger, Bradley A., Sheth, Margi, Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean Claude, Ayala, Brenda, Baboud, Julien, Chudamani, Sudha, Jensen, Mark A., Liu, Jia, Pihl, Todd, Raman, Rohini, Wan, Yunhu, Wu, Ye, Ally, Adrian, Auman, Todd J., Balasundaram, Miruna, Balu, Saianand, Baylin, Stephen B., Beroukhim, Rameen, Bootwalla, Moiz S., Bowlby, Reanne, Brooks, Denise, Butterfield, Yaron, Carlsen, Rebecca, Carter, Scott, Chin, Lynda, Chu, Andy, Chuah, Eric, Cibulskis, Kristian, Clarke, Amanda, Coetzee, Simon G., Dhalla, Noreen, Fennell, Tim, Fisher, Sheila, Gabriel, Stacey, Getz, Gad, Gibbs, Richard, Grimsby, Jonna L., Guin, Ranabir, Hadjipanayis, Angela, Hayes, Neil D., Hinoue, Toshinori, Hoadley, Katherine, Holt, Robert A., Hoyle, Alan P., Huang, Franklin, Jefferys, Stuart R., Jones, Steven, Jones, Corbin D., Kucherlapati, Raju, Lai, Phillip H., Lander, Eric, Lee, Semin, Lichtenstein, Lee, Ma, Yussanne, Maglinte, Dennis T., Mahadeshwar, Harshad S., Marra, Marco A., Mayo, Michael, Meng, Shaowu, Meyerson, Matthew L., Mieczkowski, Piotr A., Moore, Richard A., Mose, Lisle E., Mungall, Andrew J., Pantazi, Angeliki, Parfenov, Michael, Park, Peter J., Parker, Joel S., Perou, Charles M., Protopopov, Alexei, Ren, Xiaojia, Roach, Jeffrey, Rosenberg, Mara, Sabedot, Thaís S., Sadeghi, Sara, Schein, Jacqueline, Schumacher, Steven E., Seidman, Jonathan G., Seth, Sahil, Shen, Hui, Simons, Janae V., Sipahimalani, Payal, Soloway, Matthew G., Song, Xingzhi, Stewart, Chip, Sun, Huandong, Tabak, Barbara, Tam, Angela, Tan, Donghui, Tang, Jiabin, Thiessen, Nina, Triche, Timothy, Jr., Van Den Berg, David J., Veluvolu, Umadevi, Waring, Scot, Weisenberger, Daniel J., Wilkerson, Matthew D., Wong, Tina, Wu, Junyuan, Xi, Liu, Xu, Andrew W., Yang, Lixing, Zack, Travis I., Zhang, Jianhua, Aksoy, Arman B., Arachchi, Harindra, Benz, Chris, Bernard, Brady, Carlin, Daniel, Cho, Juok, DiCara, Daniel, Frazer, Scott, Fuller, Gregory N., Gao, JianJiong, Gehlenborg, Nils, Haussler, David, Heiman, David I., Iype, Lisa, Jacobsen, Anders, Ju, Zhenlin, Katzman, Sol, Kim, Hoon, Knijnenburg, Theo, Kreisberg, Richard Bailey, Lawrence, Michael S., Lee, William, Leinonen, Kalle, Lin, Pei, Ling, Shiyun, Liu, Wenbin, Liu, Yingchun, Liu, Yuexin, Lu, Yiling, Mills, Gordon, Ng, Sam, Noble, Michael S., Paull, Evan, Radenbaugh, Amie J., Rao, Arvind, Reynolds, Sheila, Saksena, Gordon, Sanborn, Zack, Sander, Chris, Schultz, Nikolaus, Senbabaoglu, Yasin, Shen, Ronglai, Shmulevich, Ilya, Sinha, Rileen, Stuart, Josh, Sumer, Onur S., Sun, Yichao, Tasman, Natalie, Taylor, Barry S., Voet, Doug, Weinhold, Nils, Weinstein, John N., Yang, Da, Zhang, Wei, Zou, Lihua, Abel, Ty, Brat, Daniel J., Cohen, Mark L., Eschbacher, Jenny, Hattab, Eyas M., Raghunathan, Aditya, Schniederjan, Matthew J., Aziz, Dina, Barnett, Gene, Barrett, Wendi, Bigner, Darell D., Boice, Lori, Brewer, Cathy, Calatozzolo, Chiara, Carlotti, Carlos Gilberto, Jr, Chan, Timothy A., Cuppini, Lucia, Curley, Erin, Cuzzubbo, Stefania, Devine, Karen, DiMeco, Francesco, Duell, Rebecca, Elder, Bradley J, Fehrenbach, Ashley, Finocchiaro, Gaetano, Friedman, William, Fulop, Jordonna, Gardner, Johanna, Hermes, Beth, Kendler, Ady, Lehman, Norman L., Lipp, Eric, Liu, Ouida, Mandt, Randy, McGraw, Mary, McLendon, Roger, McPherson, Christopher, Neder, Luciano, Nguyen, Phuong, Noss, Ardene, Nunziata, Raffaele, Ostrom, Quinn T., Palmer, Cheryl, Perin, Alessandro, Pollo, Bianca, Potapov, Alexander, Potapova, Olga, Rathmell, Kimryn W., Rotin, Daniil, Scarpace, Lisa, Schilero, Cathy, Senecal, Kelly, Shimmel, Kristen, Shurkhay, Vsevolod, Sifri, Suzanne, Singh, Rosy, Sloan, Andrew E., Smolenski, Kathy, Staugaitis, Susan M., Steele, Ruth, Thorne, Leigh, Tirapelli, Daniela P.C., Vallurupalli, Mahitha, Wang, Yun, Warnick, Ronald, Williams, Felicia, Wolinsky, Yingli, Zhang, Jianan, Bell, Sue, Campos, Benito, Herold-Mende, Christel, Jungk, Christine, and Unterberg, Andreas

Published
2015

18. Antiterrorism and Homeland Defense

Author

John G. Reynolds, Glenn E. Lawson, G. E. Southard, K. A. Van Houten, Edward W. Ott, G. M. Murray, Bradley R. Hart, Sonia E. Létant, Staci R. Kane, Masood Z. Hadi, Sharon J. Shields, Tu-Chen Cheng, Vipin K. Rastogi, J. Del Eckels, John G. Reynolds, Brandy Johnson-White, H. James Harmon, Eric J. House

Published
2007

19. Functional Beauty

Author

Murray, Bradley

Subjects
Functional Beauty (Nonfiction work) -- Book reviews, Books -- Book reviews, Philosophy and religion
Published
2010

20. Comprehensive molecular characterization of gastric adenocarcinoma

Author

Bass, Adam J., Thorsson, Vesteinn, Shmulevich, Ilya, Reynolds, Sheila M., Miller, Michael, Bernard, Brady, Hinoue, Toshinori, Laird, Peter W., Curtis, Christina, Shen, Hui, Weisenberger, Daniel J., Schultz, Nikolaus, Shen, Ronglai, Weinhold, Nils, Kelsen, David P., Bowlby, Reanne, Chu, Andy, Kasaian, Katayoon, Mungall, Andrew J., Robertson, Gordon A., Sipahimalani, Payal, Cherniack, Andrew, Getz, Gad, Liu, Yingchun, Noble, Michael S., Pedamallu, Chandra, Sougnez, Carrie, Akbani, Rehan, Lee, Ju-Seog, Liu, Wenbin, Mills, Gordon B., Yang, Da, Zhang, Wei, Pantazi, Angeliki, Gulley, Margaret, Piazuelo, Blanca M., Schneider, Barbara G., Kim, Jihun, Boussioutas, Alex, Sheth, Margi, Demchok, John A., Rabkin, Charles S., Willis, Joseph E., Ng, Sam, Garman, Katherine, Beer, David G., Pennathur, Arjun, Raphael, Benjamin J., Wu, Hsin-Ta, Odze, Robert, Kim, Hark K., Bowen, Jay, Leraas, Kristen M., Lichtenberg, Tara M., Weaver, Stephanie, McLellan, Michael, Wiznerowicz, Maciej, Sakai, Ryo, Lawrence, Michael S., Cibulskis, Kristian, Lichtenstein, Lee, Fisher, Sheila, Gabriel, Stacey B., Lander, Eric S., Ding, Li, Niu, Beifang, Ally, Adrian, Balasundaram, Miruna, Birol, Inanc, Brooks, Denise, Butterfield, Yaron S. N., Carlsen, Rebecca, Chu, Justin, Chuah, Eric, Chun, Hye-Jung E., Clarke, Amanda, Dhalla, Noreen, Guin, Ranabir, Holt, Robert A., Jones, Steven J. M., Lee, Darlene, Li, Haiyan A., Lim, Emilia, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Karen L., Nip, Ka Ming, Schein, Jacqueline E., Tam, Angela, Thiessen, Nina, Beroukhim, Rameen, Carter, Scott L., Cherniack, Andrew D., Cho, Juok, DiCara, Daniel, Frazer, Scott, Gehlenborg, Nils, Heiman, David I., Jung, Joonil, Kim, Jaegil, Lin, Pei, Meyerson, Matthew, Ojesina, Akinyemi I., Pedamallu, Chandra Sekhar, Saksena, Gordon, Schumacher, Steven E., Stojanov, Petar, Tabak, Barbara, Voet, Doug, Rosenberg, Mara, Zack, Travis I., Zhang, Hailei, Zou, Lihua, Protopopov, Alexei, Santoso, Netty, Parfenov, Michael, Lee, Semin, Zhang, Jianhua, Mahadeshwar, Harshad S., Tang, Jiabin, Ren, Xiaojia, Seth, Sahil, Yang, Lixing, Xu, Andrew W., Song, Xingzhi, Xi, Ruibin, Bristow, Christopher A., Hadjipanayis, Angela, Seidman, Jonathan, Chin, Lynda, Park, Peter J., Kucherlapati, Raju, Ling, Shiyun, Rao, Arvind, Weinstein, John N., Kim, Sang-Bae, Lu, Yiling, Mills, Gordon, Bootwalla, Moiz S., Lai, Phillip H., Triche, Timothy, Jr, Van Den Berg, David J., Baylin, Stephen B., Herman, James G., Murray, Bradley A., Askoy, Arman B., Ciriello, Giovanni, Dresdner, Gideon, Gao, Jianjiong, Gross, Benjamin, Jacobsen, Anders, Lee, William, Ramirez, Ricardo, Sander, Chris, Senbabaoglu, Yasin, Sinha, Rileen, Sumer, Onur S., Sun, Yichao, Thorsson, Vésteinn, Iype, Lisa, Kramer, Roger W., Kreisberg, Richard, Rovira, Hector, Tasman, Natalie, Haussler, David, Stuart, Josh M., Verhaak, Roeland G. W., Leiserson, Mark D. M., Taylor, Barry S., Black, Aaron D., Carney, Julie Ann, Gastier-Foster, Julie M., Helsel, Carmen, McAllister, Cynthia, Ramirez, Nilsa C., Tabler, Teresa R., Wise, Lisa, Zmuda, Erik, Penny, Robert, Crain, Daniel, Gardner, Johanna, Lau, Kevin, Curely, Erin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Shelton, Troy, Shelton, Candace, Sherman, Mark, Benz, Christopher, Lee, Jae-Hyuk, Fedosenko, Konstantin, Manikhas, Georgy, Potapova, Olga, Voronina, Olga, Belyaev, Dmitry, Dolzhansky, Oleg, Rathmell, Kimryn W., Brzezinski, Jakub, Ibbs, Matthew, Korski, Konstanty, Kycler, Witold, Łaźniak, Radoslaw, Leporowska, Ewa, Mackiewicz, Andrzej, Murawa, Dawid, Murawa, Pawel, Spychała, Arkadiusz, Suchorska, Wiktoria M., Tatka, Honorata, Teresiak, Marek, Abdel-Misih, Raafat, Bennett, Joseph, Brown, Jennifer, Iacocca, Mary, Rabeno, Brenda, Kwon, Sun-Young, Kemkes, Ariane, Curley, Erin, Alexopoulou, Iakovina, Engel, Jay, Bartlett, John, Albert, Monique, Park, Do-Youn, Dhir, Rajiv, Luketich, James, Landreneau, Rodney, Janjigian, Yelena Y., Cho, Eunjung, Ladanyi, Marc, Tang, Laura, McCall, Shannon J., Park, Young S., Cheong, Jae-Ho, Ajani, Jaffer, Camargo, Constanza M., Alonso, Shelley, Ayala, Brenda, Jensen, Mark A., Pihl, Todd, Raman, Rohini, Walton, Jessica, Wan, Yunhu, Eley, Greg, Mills Shaw, Kenna R., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean Claude, Davidsen, Tanja, Hutter, Carolyn M., Sofia, Heidi J., Burton, Robert, Chudamani, Sudha, and Liu, Jia

Published
2014
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21. Kant on genius and art

Author

Murray, Bradley

Subjects
Critique of Judgement (Book) -- Criticism and interpretation, Philosophical literature -- Criticism and interpretation, Aesthetics -- Portrayals, Arts, visual and performing, Music, Philosophy and religion
Abstract

The author examines senses of genius defined in Kant's 'Critique of Judgement'. The article supports the conclusion that to produce an artwork an agent must have and use genius in productive faculty sense, and shows that this argument was not made by Kant as generally believed.

Published
2007

22. Erratum: Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles (Cell Reports (2017) 18(11) (2780–2794) (S2211124717302140) (10.1016/j.celrep.2017.02.033))

Author

Farshidfar, Farshad, Zheng, Siyuan, Gingras, Marie-Claude, Newton, Yulia, Shih, Juliann, Robertson, A. Gordon, Hinoue, Toshinori, Hoadley, Katherine A., Gibb, Ewan A., Roszik, Jason, Covington, Kyle R., Wu, Chia-Chin, Shinbrot, Eve, Stransky, Nicolas, Hegde, Apurva, Yang, Ju Dong, Reznik, Ed, Sadeghi, Sara, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I., Hess, Julian M., Auman, J. Todd, Rhie, Suhn K., Bowlby, Reanne, Borad, Mitesh J., Akbani, Rehan, Allotey, Loretta K., Ally, Adrian, Alvaro, Domenico, Andersen, Jesper B., Appelbaum, Elizabeth L., Arora, Arshi, Balasundaram, Miruna, Balu, Saianand, Bardeesy, Nabeel, Bathe, Oliver F., Baylin, Stephen B., Beroukhim, Rameen, Berrios, Mario, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bragazzi, Maria Consiglia, Brooks, Denise, Cardinale, Vincenzo, Carlsen, Rebecca, Carpino, Guido, Carvalho, Andre L., Chaiteerakij, Roongruedee, Chandan, Vishal C., Cherniack, Andrew D., Chin, Lynda, Cho, Juok, Choe, Gina, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cordes, Matthew G., Crain, Daniel, Curley, Erin, De Rose, Agostino Maria, Defreitas, Timothy, Demchok, John A., Deshpande, Vikram, Dhalla, Noreen, Ding, Li, Evason, Kimberley, Felau, Ina, Ferguson, Martin L., Foo, Wai Chin, Franchitto, Antonio, Frazer, Scott, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Gabriel, Stacey B., Gardner, Johanna, Gastier-Foster, Julie M., Gaudio, Eugenio, Gehlenborg, Nils, Genovese, Giannicola, Gerken, Mark, Getz, Gad, Giama, Nasra H., Gibbs, Richard A., Giuliante, Felice, Grazi, Gian Luca, Hayes, D. Neil, Hegde, Apurva M., Heiman, David I., Holbrook, Andrea, Holt, Robert A., Hoyle, Alan P., Huang, Mei, Hutter, Carolyn M., Jefferys, Stuart R., Jones, Steven J. M., Jones, Corbin D., Kasaian, Katayoon, Kelley, Robin K., Kim, Jaegil, Kleiner, David E., Kocher, Jean-Pierre A., Kwong, Lawrence N., Lai, Phillip H., Laird, Peter W., Lawrence, Michael S., Leraas, Kristen M., Lichtenberg, Tara M., Lin, Pei, Liu, Wenbin, Liu, Jia, Lolla, Laxmi, Lu, Yiling, Ma, Yussanne, Mallery, David, Mardis, Elaine R., Marra, Marco A., Matsushita, Marcus M., Mayo, Michael, McLellan, Michael D., McRee, Autumn J., Meier, Sam, Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Miller, Christopher A., Mills, Gordon B., Moore, Richard A., Morris, Scott, Mose, Lisle E., Moser, Catherine D., Mounajjed, Taofic, Mungall, Andrew J., Mungall, Karen, Murray, Bradley A., Naresh, Rashi, Noble, Michael S., O'Brien, Daniel R., Parker, Joel S., Patel, Tushar C., Paulauskis, Joseph, Penny, Robert, Perou, Charles M., Perou, Amy H., Pihl, Todd, Radenbaugh, Amie J., Ramirez, Nilsa C., Rathmell, W. Kimryn, Roach, Jeffrey, Roberts, Lewis R., Saksena, Gordon, Sander, Chris, Schein, Jacqueline E., Schmidt, Heather K., Schumacher, Steven E., Shelton, Candace, Shelton, Troy, Shen, Ronglai, Sheth, Margi, Shi, Yan, Shroff, Rachna, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi J., Soloway, Matthew G., Stoppler, Hubert, Stuart, Josh, Sun, Qiang, Tam, Angela, Tan, Donghui, Tarnuzzer, Roy, Thiessen, Nina, Thorne, Leigh B., Torbenson, Michael S., Van Den Berg, David J., Veluvolu, Umadevi, Verhaak, Roel G. W., Voet, Doug, Wan, Yunhu, Wang, Zhining, Weinstein, John N., Weisenberger, Daniel J., Wheeler, David A., Wilson, Richard K., Wise, Lisa, Wong, Tina, Wu, Ye, Xi, Liu, Yang, Liming, Zenklusen, Jean C., Zhang, Hailei, Zhang, Jiashan (Julia), Zmuda, Erik, Zhu, Andrew X., Stuart, Josh M., Farshidfar, Farshad, Zheng, Siyuan, Gingras, Marie-Claude, Newton, Yulia, Shih, Juliann, Robertson, A. Gordon, Hinoue, Toshinori, Hoadley, Katherine A., Gibb, Ewan A., Roszik, Jason, Covington, Kyle R., Chia-Chin, Wu, Shinbrot, Eve, Stransky, Nicola, Hegde, Apurva, Yang, Ju Dong, Reznik, Ed, Sadeghi, Sara, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I., Hess, Julian M., Auman, J. Todd, Rhie, Suhn K., Bowlby, Reanne, Borad, Mitesh J., Akbani, Rehan, Allotey, Loretta K., Ally, Adrian, Alvaro, Domenico, Andersen, Jesper B., Appelbaum, Elizabeth L., Arora, Arshi, Balasundaram, Miruna, Balu, Saianand, Bardeesy, Nabeel, Bathe, Oliver F., Baylin, Stephen B., Beroukhim, Rameen, Berrios, Mario, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bragazzi, Maria Consiglia, Brooks, Denise, Cardinale, Vincenzo, Carlsen, Rebecca, Guido, Carpino, Carvalho, Andre L., Chaiteerakij, Roongruedee, Chandan, Vishal C., Cherniack, Andrew D., Chin, Lynda, Cho, Juok, Choe, Gina, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cordes, Matthew G., Crain, Daniel, Curley, Erin, De Rose, Agostino Maria, Defreitas, Timothy, Demchok, John A., Deshpande, Vikram, Dhalla, Noreen, Ding, Li, Evason, Kimberley, Felau, Ina, Ferguson, Martin L., Foo, Wai Chin, Franchitto, Antonio, Frazer, Scott, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Gabriel, Stacey B., Gardner, Johanna, Gastier-Foster, Julie M., Gaudio, Eugenio, Gehlenborg, Nil, Genovese, Giannicola, Gerken, Mark, Getz, Gad, Giama, Nasra H., Gibbs, Richard A., Giuliante, Felice, Grazi, Gian Luca, Hayes, D. Neil, Hegde, Apurva M., Heiman, David I., Holbrook, Andrea, Holt, Robert A., Hoyle, Alan P., Huang, Mei, Hutter, Carolyn M., Jefferys, Stuart R., Jones, Steven J. M., Jones, Corbin D., Kasaian, Katayoon, Kelley, Robin K., Kim, Jaegil, Kleiner, David E., Kocher, Jean-Pierre A., Kwong, Lawrence N., Lai, Phillip H., Laird, Peter W., Lawrence, Michael S., Leraas, Kristen M., Lichtenberg, Tara M., Lin, Pei, Liu, Wenbin, Liu, Jia, Lolla, Laxmi, Yiling, Lu, Yussanne, Ma, Mallery, David, Mardis, Elaine R., Marra, Marco A., Matsushita, Marcus M., Mayo, Michael, Mclellan, Michael D., Mcree, Autumn J., Meier, Sam, Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Miller, Christopher A., Mills, Gordon B., Moore, Richard A., Morris, Scott, Mose, Lisle E., Moser, Catherine D., Mounajjed, Taofic, Mungall, Andrew J., Mungall, Karen, Murray, Bradley A., Naresh, Rashi, Noble, Michael S., O'Brien, Daniel R., Parker, Joel S., Patel, Tushar C., Paulauskis, Joseph, Penny, Robert, Perou, Charles M., Perou, Amy H., Pihl, Todd, Radenbaugh, Amie J., Ramirez, Nilsa C., Rathmell, W. Kimryn, Roach, Jeffrey, Roberts, Lewis R., Saksena, Gordon, Sander, Chri, Schein, Jacqueline E., Schmidt, Heather K., Schumacher, Steven E., Shelton, Candace, Shelton, Troy, Shen, Ronglai, Sheth, Margi, Shi, Yan, Shroff, Rachna, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi J., Soloway, Matthew G., Stoppler, Hubert, Stuart, Josh, Sun, Qiang, Tam, Angela, Tan, Donghui, Tarnuzzer, Roy, Thiessen, Nina, Thorne, Leigh B., Torbenson, Michael S., Van Den Berg, David J., Veluvolu, Umadevi, Verhaak, Roel G. W., Voet, Doug, Wan, Yunhu, Wang, Zhining, Weinstein, John N., Weisenberger, Daniel J., Wheeler, David A., Wilson, Richard K., Wise, Lisa, Wong, Tina, Ye, Wu, Liu, Xi, Yang, Liming, Zenklusen, Jean C., Zhang, Hailei, Zhang, Jiashan (Julia), Zmuda, Erik, Zhu, Andrew X., and Stuart, Josh M.

Subjects
Genetics and Molecular Biology (all), Biochemistry, Genetics and Molecular Biology (all), Biochemistry
Abstract

Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.

Published
2017

23. A reanalysis of Schaefer et al. does not indicate extensive CRISPR/Cas9 mediated off-target editing events

Author

Murray Bradley Andrew, Reynald Lescarbeau, Nessan Bermingham, and Thomas M. Barnes

Subjects
Genetics, 0303 health sciences, Zygote, Cas9, Strain (biology), Burden of proof, Genomics, Biology, 03 medical and health sciences, 0302 clinical medicine, Variation (linguistics), Genetic variation, CRISPR, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

Recently Schaefer et al. (1) reported the presence of more than a thousand genomic differences between mice that had been edited with S. pyogenes Cas9 at the zygote stage, and a control mouse of the same strain. Given the overlap of genomic differences between the two edited mice that were not found in the control mouse, the authors concluded that these differences arose from a Cas9-dependent activity. We feel that this conclusion is inappropriate, for three key reasons: 1) there was incomplete analysis of the genetic variation; 2) there was no consideration that the variation is naturally arising in these animals; and 3) the inferred behavior of Cas9 lies outside of its understood mechanism of action. Attribution to Cas9 activity should require a burden of proof, that we believe has not been met.

Published
2017
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24. Integrated Molecular Characterization of Uterine Carcinosarcoma

Author

Kim, Jaegil, Shen, Hui, Hoffmann, Robert, Zhang, Wei, Tam, Angela, Jones, Steven J.M., Zhang, Jiashan, Walter, Vonn, David, Mutch, Wang, Chen, Weisenberger, Daniel J., Cherniack, Andrew D., Weinstein, John N., Dowdy, Sean, Soloway, Matthew G., Ling, Shiyun, Akbani, Rehan, Salvesen, Helga B., Gupta, Manaswi, Sougnez, Carrie, Jones, Corbin D., Bodenheimer, Tom, Verhaak, Roel G.W., Robertson, A. Gordon, Yang, Liming, Dhalla, Noreen, Getz, Gad, Leshchiner, Ignaty, Wong, Tina, Roach, Jeffrey, Zmuda, Erik, Laird, Peter W., Lai, Phillip H., Lawrence, Michael S., Zenklusen, Jean C., Haussler, David, Stewart, Chip, Tan, Donghui, Mungall, Andrew J., Felau, Ina, Naresh, Rashi, Thiessen, Nina, Olvera, Narciso, Schein, Jacqueline E., Liu, Jia, Brooks, Denise, Hoadley, Katherine A., Mieczkowski, Piotr A., Jefferys, Stuart R., Kandoth, Cyriac, Wu, Ye, Ramirez, Nilsa C., Rathmell, W. Kimryn, Winterhoff, Boris, Wise, Lisa, Ferguson, Martin L., Kanchi, Rupa S., Gastier-Foster, Julie M., Heiman, David I., Lander, Eric, Frazer, Scott, Marra, Marco A., Holt, Robert A., Hess, Julian, Noble, Michael S., Chudamani, Sudha, Lin, Pei, Carlsen, Rebecca, Baylin, Stephen B., Balu, Saianand, Broaddus, Russell R., Cibulskis, Kristian, Chuah, Eric, Shi, Yan, Shih, Juliann, Bogomolniy, Faina, Zhang, Hailei, Sofia, Heidi J., Sipahimalani, Payal, Zuna, Rosemary E., Hutter, Carolyn M., Levine, Douglas A., Radenbaugh, Amie J., von Bismarck, Amanda, Maglinte, Dennis T., Soslow, Robert A., Saksena, Gordon, Mayo, Michael, Auman, J. Todd, Kucherlapati, Raju, Huang, Mei, Tse, Kane, Wang, Zhining, Wan, Yunhu, Kasaian, Katayoon, Ally, Adrian, Bowlby, Reanne, Gerken, Mark, Tseng, Jill, Cline, Melissa, Veluvolu, Umadevi, Perou, Amy H., Mose, Lisle E., Skelly, Tara, Meng, Shaowu, Leraas, Kristen M., Zhu, Jing-chun, Meyerson, Matthew, Pihl, Todd, Beroukhim, Rameen, Demchok, John A., Dao, Fanny, Tarnuzzer, Roy, Lichtenberg, Tara M., Frick, Jessica, Sheth, Margi, Bowen, Jay, Zhang, Jiashan (Julia), Hoyle, Alan P., Hu, Xin, Voet, Doug, Mills, Gordon B., Hayes, D. Neil, Liu, Yuexin, Broaddus, Russell, Lee, Darlene, Kerr, Sarah, Lolla, Laxmi, Wilkerson, Matthew D., Moore, Richard A., Lu, Yiling, Bootwalla, Moiz S., Cho, Juok, Boice, Lori, Sun, Charlie, Thorne, Leigh B., Ma, Yussanne, Schumacher, Steven E., Balasundaram, Miruna, Parker, Joel S., Sadeghi, Sara, Robertson, Gordon, Liu, Wenbin, Perou, Charles M., Gehlenborg, Nils, Simons, Janae V., Murray, Bradley A., Mungall, Karen, Gabriel, Stacey, and Van Den Berg, David J.

Abstract

SummaryWe performed genomic, epigenomic, transcriptomic, and proteomic characterizations of uterine carcinosarcomas (UCSs). Cohort samples had extensive copy-number alterations and highly recurrent somatic mutations. Frequent mutations were found in TP53, PTEN, PIK3CA, PPP2R1A, FBXW7, and KRAS, similar to endometrioid and serous uterine carcinomas. Transcriptome sequencing identified a strong epithelial-to-mesenchymal transition (EMT) gene signature in a subset of cases that was attributable to epigenetic alterations at microRNA promoters. The range of EMT scores in UCS was the largest among all tumor types studied via The Cancer Genome Atlas. UCSs shared proteomic features with gynecologic carcinomas and sarcomas with intermediate EMT features. Multiple somatic mutations and copy-number alterations in genes that are therapeutic targets were identified.

Published
2017
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27. Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma

Author

Pathologie Pathologen staf, Onderzoeksgroep 6, Fishbein, Lauren, Leshchiner, Ignaty, Walter, Vonn, Danilova, Ludmila, Robertson, A. Gordon, Johnson, Amy R., Lichtenberg, Tara M., Murray, Bradley A., Ghayee, Hans K., Else, Tobias, Ling, Shiyun, Jefferys, Stuart R., de Cubas, Aguirre A., Wenz, Brandon, Korpershoek, Esther, Amelio, Antonio L., Makowski, Liza, Rathmell, W. Kimryn, Gimenez-Roqueplo, Anne Paule, Giordano, Thomas J., Asa, Sylvia L., Tischler, Arthur S., Akbani, Rehan, Ally, Adrian, Amar, Laurence, Arachchi, Harindra, Auchus, Richard J., Auman, J. Todd, Baertsch, Robert, Balasundaram, Miruna, Balu, Saianand, Bartsch, Detlef K., Baudin, Eric, Bauer, Thomas, Beaver, Allison, Benz, Christopher, Beroukhim, Rameen, Beuschlein, Felix, Bodenheimer, Tom, Boice, Lori, Bowen, Jay, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Carter, Suzie, Cassol, Clarissa A., Cherniack, Andrew D., Chin, Lynda, Cho, Juok, Chuah, Eric, Chudamani, Sudha, Cope, Leslie, Crain, Daniel, Curley, Erin, de Krijger, Ronald R., Demchok, John A., Deutschbein, Timo, Dhalla, Noreen, Dimmock, David, Dinjens, Winand N M, Eng, Charis, Eschbacher, Jennifer, Fassnacht, Martin, Felau, Ina, Feldman, Michael, Ferguson, Martin L., Fiddes, Ian, Frazer, Scott, Gabriel, Stacey B., Gardner, Johanna, Gastier-Foster, Julie M., Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Geurts, Jennifer, Goldman, Mary, Graim, Kiley, Gupta, Manaswi, Haan, David, Hahner, Stefanie, Hantel, Constanze, Haussler, David, Hayes, D. Neil, Heiman, David I., Hoadley, Katherine A., Holt, Robert A., Hoyle, Alan P., Huang, Mei, Hunt, Bryan, Hutter, Carolyn M., Jones, Steven J M, Jones, Corbin D., Kasaian, Katayoon, Kebebew, Electron, Kim, Jaegil, Kimes, Patrick, Knijnenburg, Theo, Lander, Eric, Lawrence, Michael S., Lechan, Ronald, Lee, Darlene, Leraas, Kristen M., Lerario, Antonio, Lin, Pei, Liu, Jia, LiVolsi, Virginia A., Lolla, Laxmi, Lotan, Yair, Lu, Yiling, Ma, Yussanne, Maison, Nicole, Mallery, David, Mannelli, Massimo, Marquard, Jessica, Marra, Marco A., Matthew, Thomas, Mayo, Michael, Méatchi, Tchao, Meng, Shaowu, Merino, Maria J., Mete, Ozgur, Meyerson, Matthew, Mieczkowski, Piotr A., Mills, Gordon B., Moore, Richard A., Morozova, Olena, Morris, Scott, Mose, Lisle E., Mungall, Andrew J., Naresh, Rashi, Nathanson, Katherine L., Newton, Yulia, Ng, Sam, Ni, Ying, Noble, Michael S., Nwariaku, Fiemu, Pacak, Karel, Parker, Joel S., Paul, Evan, Penny, Robert, Perou, Charles M., Perou, Amy H., Pihl, Todd, Powers, James, Rabaglia, Jennifer, Radenbaugh, Amie, Ramirez, Nilsa C., Rao, Arjun, Riester, Anna, Roach, Jeffrey, Sadeghi, Sara, Saksena, Gordon, Salama, Sofie, Saller, Charles, Sandusky, George, Sbiera, Silviu, Schein, Jacqueline E., Schumacher, Steven E., Shelton, Candace, Shelton, Troy, Sheth, Margi, Shi, Yan, Shih, Juliann, Shmulevich, Ilya, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi J., Sokolov, Artem, Soloway, Matthew G., Sougnez, Carrie, Stuart, Josh, Sun, Charlie, Swatloski, Teresa, Tam, Angela, Tan, Donghui, Tarnuzzer, Roy, Tarvin, Katherine, Thiessen, Nina, Thorne, Leigh B., Timmers, Henri J., Tse, Kane, Uzunangelov, Vlado, van Berkel, Anouk, Veluvolu, Umadevi, Vicha, Ales, Voet, Doug, Waldmann, Jens, Wan, Yunhu, Wang, Zhining, Wang, Tracy S., Weaver, Joellen, Weinstein, John N., Weismann, Dirk, Wilkerson, Matthew D., Wise, Lisa, Wong, Tina, Wong, Christopher, Wu, Ye, Yang, Liming, Zelinka, Tomas, Zenklusen, Jean C., Zhang, Jiashan (Julia), Zhang, Wei, Zhu, Jingchun, Zinzindohoué, Franck, Zmuda, Erik, Pathologie Pathologen staf, Onderzoeksgroep 6, Fishbein, Lauren, Leshchiner, Ignaty, Walter, Vonn, Danilova, Ludmila, Robertson, A. Gordon, Johnson, Amy R., Lichtenberg, Tara M., Murray, Bradley A., Ghayee, Hans K., Else, Tobias, Ling, Shiyun, Jefferys, Stuart R., de Cubas, Aguirre A., Wenz, Brandon, Korpershoek, Esther, Amelio, Antonio L., Makowski, Liza, Rathmell, W. Kimryn, Gimenez-Roqueplo, Anne Paule, Giordano, Thomas J., Asa, Sylvia L., Tischler, Arthur S., Akbani, Rehan, Ally, Adrian, Amar, Laurence, Arachchi, Harindra, Auchus, Richard J., Auman, J. Todd, Baertsch, Robert, Balasundaram, Miruna, Balu, Saianand, Bartsch, Detlef K., Baudin, Eric, Bauer, Thomas, Beaver, Allison, Benz, Christopher, Beroukhim, Rameen, Beuschlein, Felix, Bodenheimer, Tom, Boice, Lori, Bowen, Jay, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Carter, Suzie, Cassol, Clarissa A., Cherniack, Andrew D., Chin, Lynda, Cho, Juok, Chuah, Eric, Chudamani, Sudha, Cope, Leslie, Crain, Daniel, Curley, Erin, de Krijger, Ronald R., Demchok, John A., Deutschbein, Timo, Dhalla, Noreen, Dimmock, David, Dinjens, Winand N M, Eng, Charis, Eschbacher, Jennifer, Fassnacht, Martin, Felau, Ina, Feldman, Michael, Ferguson, Martin L., Fiddes, Ian, Frazer, Scott, Gabriel, Stacey B., Gardner, Johanna, Gastier-Foster, Julie M., Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Geurts, Jennifer, Goldman, Mary, Graim, Kiley, Gupta, Manaswi, Haan, David, Hahner, Stefanie, Hantel, Constanze, Haussler, David, Hayes, D. Neil, Heiman, David I., Hoadley, Katherine A., Holt, Robert A., Hoyle, Alan P., Huang, Mei, Hunt, Bryan, Hutter, Carolyn M., Jones, Steven J M, Jones, Corbin D., Kasaian, Katayoon, Kebebew, Electron, Kim, Jaegil, Kimes, Patrick, Knijnenburg, Theo, Lander, Eric, Lawrence, Michael S., Lechan, Ronald, Lee, Darlene, Leraas, Kristen M., Lerario, Antonio, Lin, Pei, Liu, Jia, LiVolsi, Virginia A., Lolla, Laxmi, Lotan, Yair, Lu, Yiling, Ma, Yussanne, Maison, Nicole, Mallery, David, Mannelli, Massimo, Marquard, Jessica, Marra, Marco A., Matthew, Thomas, Mayo, Michael, Méatchi, Tchao, Meng, Shaowu, Merino, Maria J., Mete, Ozgur, Meyerson, Matthew, Mieczkowski, Piotr A., Mills, Gordon B., Moore, Richard A., Morozova, Olena, Morris, Scott, Mose, Lisle E., Mungall, Andrew J., Naresh, Rashi, Nathanson, Katherine L., Newton, Yulia, Ng, Sam, Ni, Ying, Noble, Michael S., Nwariaku, Fiemu, Pacak, Karel, Parker, Joel S., Paul, Evan, Penny, Robert, Perou, Charles M., Perou, Amy H., Pihl, Todd, Powers, James, Rabaglia, Jennifer, Radenbaugh, Amie, Ramirez, Nilsa C., Rao, Arjun, Riester, Anna, Roach, Jeffrey, Sadeghi, Sara, Saksena, Gordon, Salama, Sofie, Saller, Charles, Sandusky, George, Sbiera, Silviu, Schein, Jacqueline E., Schumacher, Steven E., Shelton, Candace, Shelton, Troy, Sheth, Margi, Shi, Yan, Shih, Juliann, Shmulevich, Ilya, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi J., Sokolov, Artem, Soloway, Matthew G., Sougnez, Carrie, Stuart, Josh, Sun, Charlie, Swatloski, Teresa, Tam, Angela, Tan, Donghui, Tarnuzzer, Roy, Tarvin, Katherine, Thiessen, Nina, Thorne, Leigh B., Timmers, Henri J., Tse, Kane, Uzunangelov, Vlado, van Berkel, Anouk, Veluvolu, Umadevi, Vicha, Ales, Voet, Doug, Waldmann, Jens, Wan, Yunhu, Wang, Zhining, Wang, Tracy S., Weaver, Joellen, Weinstein, John N., Weismann, Dirk, Wilkerson, Matthew D., Wise, Lisa, Wong, Tina, Wong, Christopher, Wu, Ye, Yang, Liming, Zelinka, Tomas, Zenklusen, Jean C., Zhang, Jiashan (Julia), Zhang, Wei, Zhu, Jingchun, Zinzindohoué, Franck, and Zmuda, Erik

Published
2017

28. The Molecular Taxonomy of Primary Prostate Cancer

Author

Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Broad Institute of MIT and Harvard, Massachusetts Institute of Technology. Department of Biology, Bradley, Robert K, Carmell, Michelle, Carter, Scott, Chin, Lynda, Cibulskis, Kristian, Getz, Gad Asher, Heiman, David, Lander, Eric Steven, Lin, Pei, Loda, Massimo, Meyerson, Matthew L, Park, Peter J, Seidman, Jonathan, Sougnez, Carrie L, Verhaak, Roel, Voet, Douglas, Abeshouse, Adam, Ahn, Jaeil, Akbani, Rehan, Ally, Adrian, Amin, Samirkumar, Andry, Christopher D., Annala, Matti, Aprikian, Armen, Armenia, Joshua, Arora, Arshi, Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Barbieri, Christopher E., Bauer, Thomas, Benz, Christopher C., Bergeron, Alain, Beroukhim, Rameen, Berrios, Mario, Bivol, Adrian, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., dos Reis, Rodolfo Borges, Boutros, Paul C., Bowen, Jay, Bowlby, Reanne, Boyd, Jeffrey, Breggia, Anne, Brimo, Fadi, Brooks, Denise, Broom, Bradley M., Bryce, Alan H., Bubley, Glenn, Burks, Eric, Butterfield, Yaron S.N., Button, Michael, Canes, David, Carlotti, Carlos G., Carlsen, Rebecca, Carroll, Peter R., Cartun, Richard, Carver, Brett S., Chan, June M., Chang, Matthew T., Chen, Yu, Costello, Anthony J., Cherniack, Andrew D., Chevalier, Simone, Cho, Juok, Chu, Andy, Chuah, Eric, Chudamani, Sudha, Ciriello, Giovanni, Clarke, Amanda, Cooperberg, Matthew R., Corcoran, Niall M., Cowan, Janet, Crain, Daniel, Curley, Erin, David, Kerstin, Demchok, John A., Demichelis, Francesca, Dhalla, Noreen, Dhir, Rajiv, Doueik, Alexandre, Drake, Bettina, Dvinge, Heidi, Dyakova, Natalya, Felau, Ina, Ferguson, Martin L., Frazer, Scott, Freedland, Stephen, Fu, Yao, Bristow, Christopher A., Gao, Jianjiong, Gardner, Johanna, Gastier-Foster, Julie M., Gehlenborg, Nils, Gerken, Mark, Gerstein, Mark B., Godwin, Andrew K., Gopalan, Anuradha, Graefen, Markus, Graim, Kiley, Gribbin, Thomas, Guin, Ranabir, Gupta, Manaswi, Hadjipanayis, Angela, Haider, Syed, Hamel, Lucie, Hayes, D. Neil, Hess, Julian, Hoadley, Katherine A., Holbrook, Andrea H., Holt, Robert A., Holway, Antonia, Hovens, Christopher M., Hoyle, Alan P., Huang, Mei, Hutter, Carolyn M., Ittmann, Michael, Iype, Lisa, Jefferys, Stuart R., Jones, Corbin D., Jones, Steven J.M., Juhl, Hartmut, Kahles, Andre, Kane, Christopher J., Kasaian, Katayoon, Kerger, Michael, Khurana, Ekta, Kim, Jaegil, Klein, Robert J., Kucherlapati, Raju, Lacombe, Louis, Ladanyi, Marc, Lai, Phillip H., Laird, Peter W., Latour, Mathieu, Lawrence, Michael S., Lau, Kevin, LeBien, Tucker, Lee, Darlene, Lee, Semin, Lehmann, Kjong-Van, Leraas, Kristen M., Leshchiner, Ignaty, Leung, Robert, Libertino, John A., Lichtenberg, Tara M., Linehan, W. Marston, Ling, Shiyun, Lippman, Scott M., Liu, Jia, Liu, Wenbin, Lochovsky, Lucas, Logothetis, Christopher, Lolla, Laxmi, Longacre, Teri, Lu, Yiling, Luo, Jianhua, Ma, Yussanne, Mahadeshwar, Harshad S., Mallery, David, Mariamidze, Armaz, Marra, Marco A., Mayo, Michael, McCall, Shannon, McKercher, Ginette, Meng, Shaowu, Mes-Masson, Anne-Marie, Merino, Maria J., Mieczkowski, Piotr A., Mills, Gordon B., Mills Shaw, Kenna R., Minner, Sarah, Moinzadeh, Alireza, Moore, Richard A., Morris, Scott, Morrison, Carl, Mose, Lisle E., Mungall, Andrew J., Murray, Bradley A., Myers, Jerome B., Naresh, Rashi, Nelson, Joel, Nelson, Mark A., Nelson, Peter S., Newton, Yulia, Noble, Michael S., Noushmehr, Houtan, Nykter, Matti, Pantazi, Angeliki, Parfenov, Michael, Parker, Joel S., Paulauskis, Joseph, Penny, Robert, Perou, Charles M., Piche, Alain, Pihl, Todd, Pinto, Peter A., Prandi, Davide, Protopopov, Alexei, Ramirez, Nilsa C., Rao, Arvind, Rathmell, W. Kimryn, Ratsch, Gunnar, Ren, Xiaojia, Reuter, Victor E., Reynolds, Sheila M., Rhie, Suhn K., Rieger-Christ, Kimberly, Roach, Jeffrey, Robertson, A. Gordon, Robinson, Brian, Rubin, Mark A., Saad, Fred, Sadeghi, Sara, Saksena, Gordon, Saller, Charles, Salner, Andrew, Sanchez-Vega, Francisco, Sander, Chris, Sandusky, George, Sauter, Guido, Sboner, Andrea, Scardino, Peter T., Scarlata, Eleonora, Schein, Jacqueline E., Schlomm, Thorsten, Schmidt, Laura S., Schultz, Nikolaus, Schumacher, Steven E., Neder, Luciano, Seth, Sahil, Sharp, Alexis, Shelton, Candace, Shelton, Troy, Shen, Hui, Shen, Ronglai, Sherman, Mark, Sheth, Margi, Shi, Yan, Shih, Juliann, Shmulevich, Ilya, Simko, Jeffry, Simon, Ronald, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi J., Soloway, Matthew G., Song, Xingzhi, Sorcini, Andrea, Stepa, Serghei, Stewart, Chip, Stewart, John, Stuart, Joshua M., Sullivan, Travis B., Sun, Charlie, Sun, Huandong, Tam, Angela, Tan, Donghui, Tang, Jiabin, Tarnuzzer, Roy, Tarvin, Katherine, Taylor, Barry S., Teebagy, Patrick, Tenggara, Imelda, Tetu, Bernard, Tewari, Ashutosh, Thiessen, Nina, Thompson, Timothy, Thorne, Leigh B., Tirapelli, Daniela P., Tomlins, Scott A., Trevisan, Felipe Amstalden, Troncoso, Patricia, True, Lawrence D., Tsourlakis, Maria Christina, Tyekucheva, Svitlana, Van Allen, Eliezer, Van Den Berg, David J., Veluvolu, Umadevi, Vocke, Cathy D., Wan, Yunhu, Wang, Qingguo, Wang, Wenyi, Wang, Zhining, Weinhold, Nils, Weinstein, John N., Weisenberger, Daniel J., Wilkerson, Matthew D., Wise, Lisa, Witte, John, Wu, Chia-Chin, Wu, Junyuan, Wu, Ye, Xu, Andrew W., Yadav, Shalini S., Yang, Liming, Yang, Lixing, Yau, Christina, Ye, Huihui, Yena, Peggy, Zeng, Thomas, Zenklusen, Jean C., Zhang, Hailei, Zhang, Jiashan, Zhang, Wei, Zhong, Yi, Zhu, Kelsey, Zmuda, Erik, Cancer Genome Atlas Research Network, Bradley, Robert K., Meyerson, Matthew L., Park, Peter J., Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Broad Institute of MIT and Harvard, Massachusetts Institute of Technology. Department of Biology, Bradley, Robert K, Carmell, Michelle, Carter, Scott, Chin, Lynda, Cibulskis, Kristian, Getz, Gad Asher, Heiman, David, Lander, Eric Steven, Lin, Pei, Loda, Massimo, Meyerson, Matthew L, Park, Peter J, Seidman, Jonathan, Sougnez, Carrie L, Verhaak, Roel, Voet, Douglas, Abeshouse, Adam, Ahn, Jaeil, Akbani, Rehan, Ally, Adrian, Amin, Samirkumar, Andry, Christopher D., Annala, Matti, Aprikian, Armen, Armenia, Joshua, Arora, Arshi, Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Barbieri, Christopher E., Bauer, Thomas, Benz, Christopher C., Bergeron, Alain, Beroukhim, Rameen, Berrios, Mario, Bivol, Adrian, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., dos Reis, Rodolfo Borges, Boutros, Paul C., Bowen, Jay, Bowlby, Reanne, Boyd, Jeffrey, Breggia, Anne, Brimo, Fadi, Brooks, Denise, Broom, Bradley M., Bryce, Alan H., Bubley, Glenn, Burks, Eric, Butterfield, Yaron S.N., Button, Michael, Canes, David, Carlotti, Carlos G., Carlsen, Rebecca, Carroll, Peter R., Cartun, Richard, Carver, Brett S., Chan, June M., Chang, Matthew T., Chen, Yu, Costello, Anthony J., Cherniack, Andrew D., Chevalier, Simone, Cho, Juok, Chu, Andy, Chuah, Eric, Chudamani, Sudha, Ciriello, Giovanni, Clarke, Amanda, Cooperberg, Matthew R., Corcoran, Niall M., Cowan, Janet, Crain, Daniel, Curley, Erin, David, Kerstin, Demchok, John A., Demichelis, Francesca, Dhalla, Noreen, Dhir, Rajiv, Doueik, Alexandre, Drake, Bettina, Dvinge, Heidi, Dyakova, Natalya, Felau, Ina, Ferguson, Martin L., Frazer, Scott, Freedland, Stephen, Fu, Yao, Bristow, Christopher A., Gao, Jianjiong, Gardner, Johanna, Gastier-Foster, Julie M., Gehlenborg, Nils, Gerken, Mark, Gerstein, Mark B., Godwin, Andrew K., Gopalan, Anuradha, Graefen, Markus, Graim, Kiley, Gribbin, Thomas, Guin, Ranabir, Gupta, Manaswi, Hadjipanayis, Angela, Haider, Syed, Hamel, Lucie, Hayes, D. Neil, Hess, Julian, Hoadley, Katherine A., Holbrook, Andrea H., Holt, Robert A., Holway, Antonia, Hovens, Christopher M., Hoyle, Alan P., Huang, Mei, Hutter, Carolyn M., Ittmann, Michael, Iype, Lisa, Jefferys, Stuart R., Jones, Corbin D., Jones, Steven J.M., Juhl, Hartmut, Kahles, Andre, Kane, Christopher J., Kasaian, Katayoon, Kerger, Michael, Khurana, Ekta, Kim, Jaegil, Klein, Robert J., Kucherlapati, Raju, Lacombe, Louis, Ladanyi, Marc, Lai, Phillip H., Laird, Peter W., Latour, Mathieu, Lawrence, Michael S., Lau, Kevin, LeBien, Tucker, Lee, Darlene, Lee, Semin, Lehmann, Kjong-Van, Leraas, Kristen M., Leshchiner, Ignaty, Leung, Robert, Libertino, John A., Lichtenberg, Tara M., Linehan, W. Marston, Ling, Shiyun, Lippman, Scott M., Liu, Jia, Liu, Wenbin, Lochovsky, Lucas, Logothetis, Christopher, Lolla, Laxmi, Longacre, Teri, Lu, Yiling, Luo, Jianhua, Ma, Yussanne, Mahadeshwar, Harshad S., Mallery, David, Mariamidze, Armaz, Marra, Marco A., Mayo, Michael, McCall, Shannon, McKercher, Ginette, Meng, Shaowu, Mes-Masson, Anne-Marie, Merino, Maria J., Mieczkowski, Piotr A., Mills, Gordon B., Mills Shaw, Kenna R., Minner, Sarah, Moinzadeh, Alireza, Moore, Richard A., Morris, Scott, Morrison, Carl, Mose, Lisle E., Mungall, Andrew J., Murray, Bradley A., Myers, Jerome B., Naresh, Rashi, Nelson, Joel, Nelson, Mark A., Nelson, Peter S., Newton, Yulia, Noble, Michael S., Noushmehr, Houtan, Nykter, Matti, Pantazi, Angeliki, Parfenov, Michael, Parker, Joel S., Paulauskis, Joseph, Penny, Robert, Perou, Charles M., Piche, Alain, Pihl, Todd, Pinto, Peter A., Prandi, Davide, Protopopov, Alexei, Ramirez, Nilsa C., Rao, Arvind, Rathmell, W. Kimryn, Ratsch, Gunnar, Ren, Xiaojia, Reuter, Victor E., Reynolds, Sheila M., Rhie, Suhn K., Rieger-Christ, Kimberly, Roach, Jeffrey, Robertson, A. Gordon, Robinson, Brian, Rubin, Mark A., Saad, Fred, Sadeghi, Sara, Saksena, Gordon, Saller, Charles, Salner, Andrew, Sanchez-Vega, Francisco, Sander, Chris, Sandusky, George, Sauter, Guido, Sboner, Andrea, Scardino, Peter T., Scarlata, Eleonora, Schein, Jacqueline E., Schlomm, Thorsten, Schmidt, Laura S., Schultz, Nikolaus, Schumacher, Steven E., Neder, Luciano, Seth, Sahil, Sharp, Alexis, Shelton, Candace, Shelton, Troy, Shen, Hui, Shen, Ronglai, Sherman, Mark, Sheth, Margi, Shi, Yan, Shih, Juliann, Shmulevich, Ilya, Simko, Jeffry, Simon, Ronald, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi J., Soloway, Matthew G., Song, Xingzhi, Sorcini, Andrea, Stepa, Serghei, Stewart, Chip, Stewart, John, Stuart, Joshua M., Sullivan, Travis B., Sun, Charlie, Sun, Huandong, Tam, Angela, Tan, Donghui, Tang, Jiabin, Tarnuzzer, Roy, Tarvin, Katherine, Taylor, Barry S., Teebagy, Patrick, Tenggara, Imelda, Tetu, Bernard, Tewari, Ashutosh, Thiessen, Nina, Thompson, Timothy, Thorne, Leigh B., Tirapelli, Daniela P., Tomlins, Scott A., Trevisan, Felipe Amstalden, Troncoso, Patricia, True, Lawrence D., Tsourlakis, Maria Christina, Tyekucheva, Svitlana, Van Allen, Eliezer, Van Den Berg, David J., Veluvolu, Umadevi, Vocke, Cathy D., Wan, Yunhu, Wang, Qingguo, Wang, Wenyi, Wang, Zhining, Weinhold, Nils, Weinstein, John N., Weisenberger, Daniel J., Wilkerson, Matthew D., Wise, Lisa, Witte, John, Wu, Chia-Chin, Wu, Junyuan, Wu, Ye, Xu, Andrew W., Yadav, Shalini S., Yang, Liming, Yang, Lixing, Yau, Christina, Ye, Huihui, Yena, Peggy, Zeng, Thomas, Zenklusen, Jean C., Zhang, Hailei, Zhang, Jiashan, Zhang, Wei, Zhong, Yi, Zhu, Kelsey, Zmuda, Erik, Cancer Genome Atlas Research Network, Bradley, Robert K., Meyerson, Matthew L., and Park, Peter J.

Abstract

There is substantial heterogeneity among primary prostate cancers, evident in the spectrum of molecular abnormalities and its variable clinical course. As part of The Cancer Genome Atlas (TCGA), we present a comprehensive molecular analysis of 333 primary prostate carcinomas. Our results revealed a molecular taxonomy in which 74% of these tumors fell into one of seven subtypes defined by specific gene fusions (ERG, ETV1/4, and FLI1) or mutations (SPOP, FOXA1, and IDH1). Epigenetic profiles showed substantial heterogeneity, including an IDH1 mutant subset with a methylator phenotype. Androgen receptor (AR) activity varied widely and in a subtype-specific manner, with SPOP and FOXA1 mutant tumors having the highest levels of AR-induced transcripts. 25% of the prostate cancers had a presumed actionable lesion in the PI3K or MAPK signaling pathways, and DNA repair genes were inactivated in 19%. Our analysis reveals molecular heterogeneity among primary prostate cancers, as well as potentially actionable molecular defects., National Institutes of Health (U.S.). (grant 5U24CA143799), National Institutes of Health (U.S.). (grant 5U24CA143835), National Institutes of Health (U.S.). (grant 5U24CA143840), National Institutes of Health (U.S.). (grant 5U24CA143843), National Institutes of Health (U.S.). (grant 5U24CA143845), National Institutes of Health (U.S.). (grant 5U24CA143848), National Institutes of Health (U.S.). (grant 5U24CA143858), National Institutes of Health (U.S.). (grant 5U24CA143866), National Institutes of Health (U.S.). (grant 5U24CA143867), National Institutes of Health (U.S.). (grant 5U24CA143882), National Institutes of Health (U.S.). (grant 5U24CA143883), National Institutes of Health (U.S.). (grant 5U24CA144025), National Institutes of Health (U.S.). (grant U54HG003067), National Institutes of Health (U.S.). (grant U54HG003079), National Institutes of Health (U.S.). (grant U54HG003273), National Institutes of Health (U.S.). (grant P30CA16672)

Published
2017

29. Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

Author

Tirapelli, Daniel Pretti da Cunha, Cooper, Lee, Ling, Shiyun, Verhaak, Roel G.W., Zhang, Hailei, Wrensch, Margaret, Radenbaugh, Amie, Yung, W.K. Alfred, Grifford, Mia, Mikkelsen, Tom, Meyerson, Matthew, Huse, Jason, TCGA Research Network, Zoppoli, Pietro, Lau, Ching C., Barnholtz-Sloan, Jill S., Laird, Peter W., Akbani, Rehan, Anjum, Samreen, Noushmehr, Houtan, Zheng, Siyuan, Iavarone, Antonio, Malta, Tathiane, Rao, Ganesh, Rao, Aravind, Sabedot, Thais, Newton, Yulia, Carolotti, Jr., Carlos Gilberto, Rao, Arjun A., Pagnotta, Stefano, Gutmann, David, Manyam, Ganiraju, Poisson, Laila, Aldape, Kenneth, Rabadan, Raul, Murray, Bradley, Salama, Sofie, Barthel, Floris P., Haussler, David, Hess, Kenneth, Ceccarelli, Michele, Lehrman, Norman L., Cherniack, Andrew D., Morozova, Olena, Beroukhim, Rameen, Brat, Daniel J., and Wang, Jiguang

Subjects
Adult, X-linked Nuclear Protein, TCGA Research Network, Medical and Health Sciences, Promoter Regions, Rare Diseases, Genetic, Genetics, Humans, Cluster Analysis, Telomerase, Cell Proliferation, Cancer, Brain Neoplasms, Human Genome, DNA Helicases, Neurosciences, Nuclear Proteins, Glioma, Telomere, DNA Methylation, Middle Aged, Biological Sciences, Isocitrate Dehydrogenase, Brain Disorders, Brain Cancer, Orphan Drug, Mutation, Transcriptome, Signal Transduction, Epigenesis, Biotechnology, Developmental Biology
Abstract

Therapy development for adult diffuse glioma is hindered by incomplete knowledge of somatic glioma driving alterations and suboptimal disease classification. We defined the complete set of genes associated with 1,122 diffuse grade II-III-IV gliomas from The Cancer Genome Atlas and used molecular profiles to improve disease classification, identify molecular correlations, and provide insights into the progression from low- to high-grade disease. Whole-genome sequencing data analysis determined that ATRX but not TERT promoter mutations are associated with increased telomere length. Recent advances in glioma classification based on IDH mutation and 1p/19q co-deletion status were recapitulated through analysis of DNA methylation profiles, which identified clinically relevant molecular subsets. A subtype of IDH mutant glioma was associated with DNA demethylation and poor outcome; a group of IDH-wild-type diffuse glioma showed molecular similarity to pilocytic astrocytoma and relatively favorable survival. Understanding of cohesive disease groups may aid improved clinical outcomes.

Published
2016

30. Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma

Author

Raphael, Benjamin J., primary, Hruban, Ralph H., additional, Aguirre, Andrew J., additional, Moffitt, Richard A., additional, Yeh, Jen Jen, additional, Stewart, Chip, additional, Robertson, A. Gordon, additional, Cherniack, Andrew D., additional, Gupta, Manaswi, additional, Getz, Gad, additional, Gabriel, Stacey B., additional, Meyerson, Matthew, additional, Cibulskis, Carrie, additional, Fei, Suzanne S., additional, Hinoue, Toshinori, additional, Shen, Hui, additional, Laird, Peter W., additional, Ling, Shiyun, additional, Lu, Yiling, additional, Mills, Gordon B., additional, Akbani, Rehan, additional, Loher, Phillipe, additional, Londin, Eric R., additional, Rigoutsos, Isidore, additional, Telonis, Aristeidis G., additional, Gibb, Ewan A., additional, Goldenberg, Anna, additional, Mezlini, Aziz M., additional, Hoadley, Katherine A., additional, Collisson, Eric, additional, Lander, Eric, additional, Murray, Bradley A., additional, Hess, Julian, additional, Rosenberg, Mara, additional, Bergelson, Louis, additional, Zhang, Hailei, additional, Cho, Juok, additional, Tiao, Grace, additional, Kim, Jaegil, additional, Livitz, Dimitri, additional, Leshchiner, Ignaty, additional, Reardon, Brendan, additional, Van Allen, Eliezer, additional, Kamburov, Atanas, additional, Beroukhim, Rameen, additional, Saksena, Gordon, additional, Schumacher, Steven E., additional, Noble, Michael S., additional, Heiman, David I., additional, Gehlenborg, Nils, additional, Lawrence, Michael S., additional, Adsay, Volkan, additional, Petersen, Gloria, additional, Klimstra, David, additional, Bardeesy, Nabeel, additional, Leiserson, Mark D.M., additional, Bowlby, Reanne, additional, Kasaian, Katayoon, additional, Birol, Inanc, additional, Mungall, Karen L., additional, Sadeghi, Sara, additional, Weinstein, John N., additional, Spellman, Paul T., additional, Liu, Yuexin, additional, Amundadottir, Laufey T., additional, Tepper, Joel, additional, Singhi, Aatur D., additional, Dhir, Rajiv, additional, Paul, Drwiega, additional, Smyrk, Thomas, additional, Zhang, Lizhi, additional, Kim, Paula, additional, Bowen, Jay, additional, Frick, Jessica, additional, Gastier-Foster, Julie M., additional, Gerken, Mark, additional, Lau, Kevin, additional, Leraas, Kristen M., additional, Lichtenberg, Tara M., additional, Ramirez, Nilsa C., additional, Renkel, Jeremy, additional, Sherman, Mark, additional, Wise, Lisa, additional, Yena, Peggy, additional, Zmuda, Erik, additional, Shih, Juliann, additional, Ally, Adrian, additional, Balasundaram, Miruna, additional, Carlsen, Rebecca, additional, Chu, Andy, additional, Chuah, Eric, additional, Clarke, Amanda, additional, Dhalla, Noreen, additional, Holt, Robert A., additional, Jones, Steven J.M., additional, Lee, Darlene, additional, Ma, Yussanne, additional, Marra, Marco A., additional, Mayo, Michael, additional, Moore, Richard A., additional, Mungall, Andrew J., additional, Schein, Jacqueline E., additional, Sipahimalani, Payal, additional, Tam, Angela, additional, Thiessen, Nina, additional, Tse, Kane, additional, Wong, Tina, additional, Brooks, Denise, additional, Auman, J. Todd, additional, Balu, Saianand, additional, Bodenheimer, Tom, additional, Hayes, D. Neil, additional, Hoyle, Alan P., additional, Jefferys, Stuart R., additional, Jones, Corbin D., additional, Meng, Shaowu, additional, Mieczkowski, Piotr A., additional, Mose, Lisle E., additional, Perou, Charles M., additional, Perou, Amy H., additional, Roach, Jeffrey, additional, Shi, Yan, additional, Simons, Janae V., additional, Skelly, Tara, additional, Soloway, Matthew G., additional, Tan, Donghui, additional, Veluvolu, Umadevi, additional, Parker, Joel S., additional, Wilkerson, Matthew D., additional, Korkut, Anil, additional, Senbabaoglu, Yasin, additional, Burch, Patrick, additional, McWilliams, Robert, additional, Chaffee, Kari, additional, Oberg, Ann, additional, Zhang, Wei, additional, Gingras, Marie-Claude, additional, Wheeler, David A., additional, Xi, Liu, additional, Albert, Monique, additional, Bartlett, John, additional, Sekhon, Harman, additional, Stephen, Yeager, additional, Howard, Zaren, additional, Judy, Miller, additional, Breggia, Anne, additional, Shroff, Rachna T., additional, Chudamani, Sudha, additional, Liu, Jia, additional, Lolla, Laxmi, additional, Naresh, Rashi, additional, Pihl, Todd, additional, Sun, Qiang, additional, Wan, Yunhu, additional, Wu, Ye, additional, Jennifer, Smith, additional, Roggin, Kevin, additional, Becker, Karl-Friedrich, additional, Behera, Madhusmita, additional, Bennett, Joseph, additional, Boice, Lori, additional, Burks, Eric, additional, Carlotti Junior, Carlos Gilberto, additional, Chabot, John, additional, Pretti da Cunha Tirapelli, Daniela, additional, Sebastião dos Santos, Jose, additional, Dubina, Michael, additional, Eschbacher, Jennifer, additional, Huang, Mei, additional, Huelsenbeck-Dill, Lori, additional, Jenkins, Roger, additional, Karpov, Alexey, additional, Kemp, Rafael, additional, Lyadov, Vladimir, additional, Maithel, Shishir, additional, Manikhas, Georgy, additional, Montgomery, Eric, additional, Noushmehr, Houtan, additional, Osunkoya, Adeboye, additional, Owonikoko, Taofeek, additional, Paklina, Oxana, additional, Potapova, Olga, additional, Ramalingam, Suresh, additional, Rathmell, W. Kimryn, additional, Rieger-Christ, Kimberly, additional, Saller, Charles, additional, Setdikova, Galiya, additional, Shabunin, Alexey, additional, Sica, Gabriel, additional, Su, Tao, additional, Sullivan, Travis, additional, Swanson, Pat, additional, Tarvin, Katherine, additional, Tavobilov, Michael, additional, Thorne, Leigh B., additional, Urbanski, Stefan, additional, Voronina, Olga, additional, Wang, Timothy, additional, Crain, Daniel, additional, Curley, Erin, additional, Gardner, Johanna, additional, Mallery, David, additional, Morris, Scott, additional, Paulauskis, Joseph, additional, Penny, Robert, additional, Shelton, Candace, additional, Shelton, Troy, additional, Janssen, Klaus-Peter, additional, Bathe, Oliver, additional, Bahary, Nathan, additional, Slotta-Huspenina, Julia, additional, Johns, Amber, additional, Hibshoosh, Hanina, additional, Hwang, Rosa F., additional, Sepulveda, Antonia, additional, Radenbaugh, Amie, additional, Baylin, Stephen B., additional, Berrios, Mario, additional, Bootwalla, Moiz S., additional, Holbrook, Andrea, additional, Lai, Phillip H., additional, Maglinte, Dennis T., additional, Mahurkar, Swapna, additional, Triche, Timothy J., additional, Van Den Berg, David J., additional, Weisenberger, Daniel J., additional, Chin, Lynda, additional, Kucherlapati, Raju, additional, Kucherlapati, Melanie, additional, Pantazi, Angeliki, additional, Park, Peter, additional, Voet, Doug, additional, Lin, Pei, additional, Frazer, Scott, additional, Defreitas, Timothy, additional, Meier, Sam, additional, Kwon, Sun Young, additional, Kim, Yong Hoon, additional, Park, Sang-Jae, additional, Han, Sung-Sik, additional, Kim, Seong Hoon, additional, Kim, Hark, additional, Furth, Emma, additional, Tempero, Margaret, additional, Sander, Chris, additional, Biankin, Andrew, additional, Chang, David, additional, Bailey, Peter, additional, Gill, Anthony, additional, Kench, James, additional, Grimmond, Sean, additional, Cancer Genome Initiative (APGI, Australian Pancreatic, additional, Postier, Russell, additional, Zuna, Rosemary, additional, Sicotte, Hugues, additional, Demchok, John A., additional, Ferguson, Martin L., additional, Hutter, Carolyn M., additional, Mills Shaw, Kenna R., additional, Sheth, Margi, additional, Sofia, Heidi J., additional, Tarnuzzer, Roy, additional, Wang, Zhining, additional, Yang, Liming, additional, Zhang, Jiashan (Julia), additional, Felau, Ina, additional, and Zenklusen, Jean C., additional

Published
2017
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31. Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma

Author

Robertson, A. Gordon, primary, Shih, Juliann, additional, Yau, Christina, additional, Gibb, Ewan A., additional, Oba, Junna, additional, Mungall, Karen L., additional, Hess, Julian M., additional, Uzunangelov, Vladislav, additional, Walter, Vonn, additional, Danilova, Ludmila, additional, Lichtenberg, Tara M., additional, Kucherlapati, Melanie, additional, Kimes, Patrick K., additional, Tang, Ming, additional, Penson, Alexander, additional, Babur, Ozgun, additional, Akbani, Rehan, additional, Bristow, Christopher A., additional, Hoadley, Katherine A., additional, Iype, Lisa, additional, Chang, Matthew T., additional, Cherniack, Andrew D., additional, Benz, Christopher, additional, Mills, Gordon B., additional, Verhaak, Roel G.W., additional, Griewank, Klaus G., additional, Felau, Ina, additional, Zenklusen, Jean C., additional, Gershenwald, Jeffrey E., additional, Schoenfield, Lynn, additional, Lazar, Alexander J., additional, Abdel-Rahman, Mohamed H., additional, Roman-Roman, Sergio, additional, Stern, Marc-Henri, additional, Cebulla, Colleen M., additional, Williams, Michelle D., additional, Jager, Martine J., additional, Coupland, Sarah E., additional, Esmaeli, Bita, additional, Kandoth, Cyriac, additional, Woodman, Scott E., additional, Ally, Adrian, additional, Auman, J. Todd, additional, Balasundaram, Miruna, additional, Balu, Saianand, additional, Beroukhim, Rameen, additional, Birol, Inanc, additional, Bodenheimer, Tom, additional, Bowen, Jay, additional, Bowlby, Reanne, additional, Brooks, Denise, additional, Carlsen, Rebecca, additional, Chin, Lynda, additional, Cho, Juok, additional, Chuah, Eric, additional, Chudamani, Sudha, additional, Cibulskis, Carrie, additional, Cibulskis, Kristian, additional, Cope, Leslie, additional, Defreitas, Timothy, additional, Demchok, John A., additional, Desjardins, Laurence, additional, Dhalla, Noreen, additional, Ferguson, Martin L., additional, Frazer, Scott, additional, Gabriel, Stacey B., additional, Gastier-Foster, Julie M., additional, Gehlenborg, Nils, additional, Gerken, Mark, additional, Getz, Gad, additional, Grimm, Elizabeth A., additional, Hayes, D. Neil, additional, Hegde, Apurva M., additional, Heiman, David I., additional, Helsel, Carmen, additional, Hobensack, Shital, additional, Holt, Robert A., additional, Hoyle, Alan P., additional, Hu, Xin, additional, Hutter, Carolyn M., additional, Jefferys, Stuart R., additional, Jones, Corbin D., additional, Jones, Steven J.M., additional, Kasaian, Katayoon, additional, Kim, Jaegil, additional, Kucherlapati, Raju, additional, Lander, Eric, additional, Lawrence, Michael S., additional, Lee, Semin, additional, Leraas, Kristen M., additional, Lin, Pei, additional, Liu, Jia, additional, Liu, Wenbin, additional, Lolla, Laxmi, additional, Lu, Yiling, additional, Ma, Yussanne, additional, Mahadeshwar, Harshad S., additional, Mariani, Odette, additional, Marra, Marco A., additional, Mayo, Michael, additional, Meier, Sam, additional, Meng, Shaowu, additional, Meyerson, Matthew, additional, Mieczkowski, Piotr A., additional, Moore, Richard A., additional, Mose, Lisle E., additional, Mungall, Andrew J., additional, Murray, Bradley A., additional, Naresh, Rashi, additional, Noble, Michael S., additional, Pantazi, Angeliki, additional, Parfenov, Michael, additional, Park, Peter J., additional, Parker, Joel S., additional, Perou, Charles M., additional, Pihl, Todd, additional, Pilarski, Robert, additional, Protopopov, Alexei, additional, Radenbaugh, Amie, additional, Rai, Karan, additional, Ramirez, Nilsa C., additional, Ren, Xiaojia, additional, Reynolds, Sheila M., additional, Roach, Jeffrey, additional, Robertson, A. Gordon, additional, Roszik, Jason, additional, Sadeghi, Sara, additional, Saksena, Gordon, additional, Sastre, Xavier, additional, Schadendorf, Dirk, additional, Schein, Jacqueline E., additional, Schumacher, Steven E., additional, Seidman, Jonathan, additional, Seth, Sahil, additional, Sethi, Geetika, additional, Sheth, Margi, additional, Shi, Yan, additional, Shields, Carol, additional, Shmulevich, Ilya, additional, Simons, Janae V., additional, Singh, Arun D., additional, Sipahimalani, Payal, additional, Skelly, Tara, additional, Sofia, Heidi, additional, Soloway, Matthew G., additional, Song, Xingzhi, additional, Stuart, Joshua, additional, Sun, Qiang, additional, Sun, Huandong, additional, Tam, Angela, additional, Tan, Donghui, additional, Tang, Jiabin, additional, Tarnuzzer, Roy, additional, Taylor, Barry S., additional, Thiessen, Nina, additional, Thorsson, Vesteinn, additional, Tse, Kane, additional, Veluvolu, Umadevi, additional, Voet, Doug, additional, Wan, Yunhu, additional, Wang, Zhining, additional, Weinstein, John N., additional, Wilkerson, Matthew D., additional, Wise, Lisa, additional, Wong, Tina, additional, Wu, Ye, additional, Yang, Liming, additional, Yang, Lixing, additional, Zhang, Jiashan, additional, Zhang, Hailei, additional, and Zmuda, Erik, additional

Published
2017
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33. Characterising cis-regulatory variation in the transcriptome of histologically normal and tumour-derived pancreatic tissues

Author

Zhang, Mingfeng, primary, Lykke-Andersen, Soren, additional, Zhu, Bin, additional, Xiao, Wenming, additional, Hoskins, Jason W, additional, Zhang, Xijun, additional, Rost, Lauren M, additional, Collins, Irene, additional, Bunt, Martijn van de, additional, Jia, Jinping, additional, Parikh, Hemang, additional, Zhang, Tongwu, additional, Song, Lei, additional, Jermusyk, Ashley, additional, Chung, Charles C, additional, Zhou, Weiyin, additional, Matters, Gail L, additional, Kurtz, Robert C, additional, Yeager, Meredith, additional, Jensen, Torben Heick, additional, Brown, Kevin M, additional, Ongen, Halit, additional, Bamlet, William R, additional, Murray, Bradley A, additional, McCarthy, Mark I, additional, Chanock, Stephen J, additional, Chatterjee, Nilanjan, additional, Wolpin, Brian M, additional, Smith, Jill P, additional, Olson, Sara H, additional, Petersen, Gloria M, additional, Shi, Jianxin, additional, and Amundadottir, Laufey, additional

Published
2017
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34. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles

Author

Farshidfar, Farshad, primary, Zheng, Siyuan, additional, Gingras, Marie-Claude, additional, Newton, Yulia, additional, Shih, Juliann, additional, Robertson, A. Gordon, additional, Hinoue, Toshinori, additional, Hoadley, Katherine A., additional, Gibb, Ewan A., additional, Roszik, Jason, additional, Covington, Kyle R., additional, Wu, Chia-Chin, additional, Shinbrot, Eve, additional, Stransky, Nicolas, additional, Hegde, Apurva, additional, Yang, Ju Dong, additional, Reznik, Ed, additional, Sadeghi, Sara, additional, Pedamallu, Chandra Sekhar, additional, Ojesina, Akinyemi I., additional, Hess, Julian M., additional, Auman, J. Todd, additional, Rhie, Suhn K., additional, Bowlby, Reanne, additional, Borad, Mitesh J., additional, Zhu, Andrew X., additional, Stuart, Josh M., additional, Sander, Chris, additional, Akbani, Rehan, additional, Cherniack, Andrew D., additional, Deshpande, Vikram, additional, Mounajjed, Taofic, additional, Foo, Wai Chin, additional, Torbenson, Michael S., additional, Kleiner, David E., additional, Laird, Peter W., additional, Wheeler, David A., additional, McRee, Autumn J., additional, Bathe, Oliver F., additional, Andersen, Jesper B., additional, Bardeesy, Nabeel, additional, Roberts, Lewis R., additional, Kwong, Lawrence N., additional, Allotey, Loretta K., additional, Ally, Adrian, additional, Alvaro, Domenico, additional, Appelbaum, Elizabeth L., additional, Arora, Arshi, additional, Balasundaram, Miruna, additional, Balu, Saianand, additional, Baylin, Stephen B., additional, Beroukhim, Rameen, additional, Berrios, Mario, additional, Bodenheimer, Tom, additional, Boice, Lori, additional, Bootwalla, Moiz S., additional, Bowen, Jay, additional, Bragazzi, Maria Consiglia, additional, Brooks, Denise, additional, Cardinale, Vincenzo, additional, Carlsen, Rebecca, additional, Carpino, Guido, additional, Carvalho, Andre L., additional, Chaiteerakij, Roongruedee, additional, Chandan, Vishal C., additional, Chin, Lynda, additional, Cho, Juok, additional, Choe, Gina, additional, Chuah, Eric, additional, Chudamani, Sudha, additional, Cibulskis, Carrie, additional, Cordes, Matthew G., additional, Crain, Daniel, additional, Curley, Erin, additional, De Rose, Agostino Maria, additional, Defreitas, Timothy, additional, Demchok, John A., additional, Dhalla, Noreen, additional, Ding, Li, additional, Evason, Kimberley, additional, Farshidfar, Farshad, additional, Felau, Ina, additional, Ferguson, Martin L., additional, Franchitto, Antonio, additional, Frazer, Scott, additional, Fronick, Catrina C., additional, Fulton, Lucinda A., additional, Fulton, Robert S., additional, Gabriel, Stacey B., additional, Gardner, Johanna, additional, Gastier-Foster, Julie M., additional, Gaudio, Eugenio, additional, Gehlenborg, Nils, additional, Genovese, Giannicola, additional, Gerken, Mark, additional, Getz, Gad, additional, Giama, Nasra H., additional, Gibbs, Richard A., additional, Giuliante, Felice, additional, Grazi, Gian Luca, additional, Hayes, D. Neil, additional, Hegde, Apurva M., additional, Heiman, David I., additional, Holbrook, Andrea, additional, Holt, Robert A., additional, Hoyle, Alan P., additional, Huang, Mei, additional, Hutter, Carolyn M., additional, Jefferys, Stuart R., additional, Jones, Steven J.M., additional, Jones, Corbin D., additional, Kasaian, Katayoon, additional, Kelley, Robin K., additional, Kim, Jaegil, additional, Kocher, Jean-Pierre A., additional, Lai, Phillip H., additional, Lawrence, Michael S., additional, Leraas, Kristen M., additional, Lichtenberg, Tara M., additional, Lin, Pei, additional, Liu, Wenbin, additional, Liu, Jia, additional, Lolla, Laxmi, additional, Lu, Yiling, additional, Ma, Yussanne, additional, Mallery, David, additional, Mardis, Elaine R., additional, Marra, Marco A., additional, Matsushita, Marcus M., additional, Mayo, Michael, additional, McLellan, Michael D., additional, Meier, Sam, additional, Meng, Shaowu, additional, Meyerson, Matthew, additional, Mieczkowski, Piotr A., additional, Miller, Christopher A., additional, Mills, Gordon B., additional, Moore, Richard A., additional, Morris, Scott, additional, Mose, Lisle E., additional, Moser, Catherine D., additional, Mungall, Andrew J., additional, Mungall, Karen, additional, Murray, Bradley A., additional, Naresh, Rashi, additional, Noble, Michael S., additional, O’Brien, Daniel R., additional, Parker, Joel S., additional, Patel, Tushar C., additional, Paulauskis, Joseph, additional, Penny, Robert, additional, Perou, Charles M., additional, Perou, Amy H., additional, Pihl, Todd, additional, Radenbaugh, Amie J., additional, Ramirez, Nilsa C., additional, Rathmell, W. Kimryn, additional, Roach, Jeffrey, additional, Saksena, Gordon, additional, Schein, Jacqueline E., additional, Schmidt, Heather K., additional, Schumacher, Steven E., additional, Shelton, Candace, additional, Shelton, Troy, additional, Shen, Ronglai, additional, Sheth, Margi, additional, Shi, Yan, additional, Shroff, Rachna, additional, Simons, Janae V., additional, Sipahimalani, Payal, additional, Skelly, Tara, additional, Sofia, Heidi J., additional, Soloway, Matthew G., additional, Stoppler, Hubert, additional, Stuart, Josh, additional, Sun, Qiang, additional, Tam, Angela, additional, Tan, Donghui, additional, Tarnuzzer, Roy, additional, Thiessen, Nina, additional, Thorne, Leigh B., additional, Van Den Berg, David J., additional, Veluvolu, Umadevi, additional, Verhaak, Roel G.W., additional, Voet, Doug, additional, Wan, Yunhu, additional, Wang, Zhining, additional, Weinstein, John N., additional, Weisenberger, Daniel J., additional, Wilson, Richard K., additional, Wise, Lisa, additional, Wong, Tina, additional, Wu, Ye, additional, Xi, Liu, additional, Yang, Liming, additional, Zenklusen, Jean C., additional, Zhang, Hailei, additional, Zhang, Jiashan (Julia), additional, and Zmuda, Erik, additional

Published
2017
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35. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

Author

Cancer Genome Atlas Research Network, Brat, Daniel J, Verhaak, Roel GW, Aldape, Kenneth D, Yung, WK Alfred, Salama, Sofie R, Cooper, Lee AD, Rheinbay, Esther, Miller, C Ryan, Vitucci, Mark, Morozova, Olena, Robertson, A Gordon, Noushmehr, Houtan, Laird, Peter W, Cherniack, Andrew D, Akbani, Rehan, Huse, Jason T, Ciriello, Giovanni, Poisson, Laila M, Barnholtz-Sloan, Jill S, Berger, Mitchel S, Brennan, Cameron, Colen, Rivka R, Colman, Howard, Flanders, Adam E, Giannini, Caterina, Grifford, Mia, Iavarone, Antonio, Jain, Rajan, Joseph, Isaac, Kim, Jaegil, Kasaian, Katayoon, Mikkelsen, Tom, Murray, Bradley A, O'Neill, Brian Patrick, Pachter, Lior, Parsons, Donald W, Sougnez, Carrie, Sulman, Erik P, Vandenberg, Scott R, Van Meir, Erwin G, von Deimling, Andreas, Zhang, Hailei, Crain, Daniel, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Troy, Sherman, Mark, Yena, Peggy, Black, Aaron, Bowen, Jay, Dicostanzo, Katie, Gastier-Foster, Julie, Leraas, Kristen M, Lichtenberg, Tara M, Pierson, Christopher R, Ramirez, Nilsa C, Taylor, Cynthia, Weaver, Stephanie, Wise, Lisa, Zmuda, Erik, Davidsen, Tanja, Demchok, John A, Eley, Greg, Ferguson, Martin L, Hutter, Carolyn M, Mills Shaw, Kenna R, Ozenberger, Bradley A, Sheth, Margi, Sofia, Heidi J, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean Claude, Ayala, Brenda, Baboud, Julien, Chudamani, Sudha, Jensen, Mark A, Liu, Jia, Pihl, Todd, Raman, Rohini, Wan, Yunhu, Wu, Ye, Ally, Adrian, Auman, J Todd, Balasundaram, Miruna, Balu, Saianand, Baylin, Stephen B, Beroukhim, Rameen, Bootwalla, Moiz S, Bowlby, Reanne, Bristow, Christopher A, Brooks, Denise, Butterfield, Yaron, Carlsen, Rebecca, Carter, Scott, and Chin, Lynda

Subjects
p53, Adult, Male, Adolescent, Cancer Genome Atlas Research Network, Kaplan-Meier Estimate, Medical and Health Sciences, Chromosomes, Rare Diseases, General & Internal Medicine, Genetics, Humans, Cluster Analysis, Proportional Hazards Models, Aged, Cancer, Pair 19, Human Genome, Glioma, DNA, Middle Aged, Brain Disorders, Brain Cancer, Genes, Mutation, Pair 1, Neoplasm, Female, Neoplasm Grading, Glioblastoma, Sequence Analysis, Human, Signal Transduction
Abstract

BackgroundDiffuse low-grade and intermediate-grade gliomas (which together make up the lower-grade gliomas, World Health Organization grades II and III) have highly variable clinical behavior that is not adequately predicted on the basis of histologic class. Some are indolent; others quickly progress to glioblastoma. The uncertainty is compounded by interobserver variability in histologic diagnosis. Mutations in IDH, TP53, and ATRX and codeletion of chromosome arms 1p and 19q (1p/19q codeletion) have been implicated as clinically relevant markers of lower-grade gliomas.MethodsWe performed genomewide analyses of 293 lower-grade gliomas from adults, incorporating exome sequence, DNA copy number, DNA methylation, messenger RNA expression, microRNA expression, and targeted protein expression. These data were integrated and tested for correlation with clinical outcomes.ResultsUnsupervised clustering of mutations and data from RNA, DNA-copy-number, and DNA-methylation platforms uncovered concordant classification of three robust, nonoverlapping, prognostically significant subtypes of lower-grade glioma that were captured more accurately by IDH, 1p/19q, and TP53 status than by histologic class. Patients who had lower-grade gliomas with an IDH mutation and 1p/19q codeletion had the most favorable clinical outcomes. Their gliomas harbored mutations in CIC, FUBP1, NOTCH1, and the TERT promoter. Nearly all lower-grade gliomas with IDH mutations and no 1p/19q codeletion had mutations in TP53 (94%) and ATRX inactivation (86%). The large majority of lower-grade gliomas without an IDH mutation had genomic aberrations and clinical behavior strikingly similar to those found in primary glioblastoma.ConclusionsThe integration of genomewide data from multiple platforms delineated three molecular classes of lower-grade gliomas that were more concordant with IDH, 1p/19q, and TP53 status than with histologic class. Lower-grade gliomas with an IDH mutation either had 1p/19q codeletion or carried a TP53 mutation. Most lower-grade gliomas without an IDH mutation were molecularly and clinically similar to glioblastoma. (Funded by the National Institutes of Health.).

Published
2015

36. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer

Author

Gehlenborg, Nils, Mills, Gordon B., Ramirez, Nilsa C., Mungall, Andrew J., Zhang, Hailei, Schultz, Nikolaus, Ding, Li, Wang, Zhining, Sofia, Heidi J., Felau, Ina, Murray, Bradley A., Wiznerowicz, MacIej, Brooks, Denise, Yang, Liming, Shriver, Craig, Chin, Lynda, Jefferys, Stuart R., Perou, Charles M., Gibson, William J., Holbrook, Andrea, Jones, Steven J.M., Shi, Yan, Gatza, Michael L., Tarnuzzer, Roy, Roach, Jeffrey, Gabriel, Stacey B., Shaw, Kenna R.Mills, Beroukhim, Rameen, Robertson, A. Gordon, Hoyle, Alan P., Lolla, Laxmi, Holt, Robert A., Olopade, Olufunmilayo, Wu, Junyuan, Zack, Travis I., Davidsen, Tanja, Naresh, Rashi, Kim, Jaegil, Liu, Wenbin, Gastier-Foster, Julie M., Liu, Jia, Pastore, Alessandro, Wilson, Richard, Frazer, Scott, Benz, Christopher, Huang, Mei, Schein, Jacqueline E., Kandoth, Cyriac, Rhie, Suhn K., Soloway, Matthew G., Hwang, E. Shelley, Boice, Lori, Cho, Juok, Meyerson, Matthew, Benz, Stephen, Saksena, Gordon, Fieldhouse, Robert, Hu, Hai, Leraas, Kristen M., Laird, Peter W., King, Tari A., Getz, Gad, Ju, Zhenlin, Johnson, Nicole B., McAllister, Cynthia, Pihl, Todd, Marks, Jeffrey, Sun, Charlie, Wise, Lisa, Ling, Shiyun, Lichtenberg, Tara M., Barr, Thomas, Balasundaram, Miruna, Gerken, Mark, Weinstein, John N., Lester, Susan C., Weisenberger, Daniel J., Tse, Gary M.K., Zhang, Jiashan, Marra, Marco A., Shen, Hui, Sander, Chris, Chudamani, Sudha, Zmuda, Erik, Parker, Joel S., Collins, Laura C., Tiezzi, Daniel G., Hutter, Carolyn M., Zenklusen, Jean C., Sougnez, Carrie, Lawrence, Michael S., Lu, Yiling, Bowlby, Reanne, Robertson, Gordon, Moore, Richard A., Simons, Janae V., Bootwalla, Moiz S., Meng, Shaowu, Cherniack, Andrew D., Shih, Juliann, Hoadley, Katherine A., Berrios, Mario, Auman, J. Todd, Akbani, Rehan, Beck, Andrew H., McLellan, Michael, Demchok, John A., Maglinte, Dennis T., Schumacher, Steven E., Lai, Phillip H., Bodenheimer, Tom, Allison, Kimberly H., Bowen, Jay, Yau, Christina, Gao, Jian Jiong, Ferguson, Martin L., Mose, Lisle E., Sheth, Margi, Jensen, Kristin, Mardis, Elaine, Van Den Berg, David J., Voet, Doug, Heiman, David I., Hayes, D. Neil, Oesterreich, Steffi, Rathmell, W. Kimryn, Wilkerson, Matthew D., Lin, Pei, Ma, Yussanne, Hayat, Sikander, Balu, Saianand, Noble, Michael S., Shelley, Carl Simon, Chen, Yunn Yi, Factor, Rachel E., Wu, Ye, Wan, Yunhu, Ciriello, Giovanni, and Dennison, Jennifer B.

Subjects
body regions, skin and connective tissue diseases
Abstract

Invasive lobular carcinoma (ILC) is the second most prevalent histologic subtype of invasive breast cancer. Here, we comprehensively profiled 817 breast tumors, including 127 ILC, 490 ductal (IDC), and 88 mixed IDC/ILC. Besides E-cadherin loss, the best known ILC genetic hallmark, we identified mutations targeting PTEN, TBX3 and FOXA1 as ILC enriched features. PTEN loss associated with increased AKT phosphorylation, which was highest in ILC among all breast cancer subtypes. Spatially clustered FOXA1 mutations correlated with increased FOXA1 expression and activity. Conversely, GATA3 mutations and high expression characterized Luminal A IDC, suggesting differential modulation of ER activity in ILC and IDC. Proliferation and immune-related signatures determined three ILC transcriptional subtypes associated with survival differences. Mixed IDC/ILC cases were molecularly classified as ILC-like and IDC-like revealing no true hybrid features. This multidimensional molecular atlas sheds new light on the genetic bases of ILC and provides potential clinical options.

Published
2015
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37. Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.

Author

Cancer Genome Atlas Research Network, Cancer Genome Atlas Research Network, Linehan, W Marston, Spellman, Paul T, Ricketts, Christopher J, Creighton, Chad J, Fei, Suzanne S, Davis, Caleb, Wheeler, David A, Murray, Bradley A, Schmidt, Laura, Vocke, Cathy D, Peto, Myron, Al Mamun, Abu Amar M, Shinbrot, Eve, Sethi, Anurag, Brooks, Samira, Rathmell, W Kimryn, Brooks, Angela N, Hoadley, Katherine A, Robertson, A Gordon, Brooks, Denise, Bowlby, Reanne, Sadeghi, Sara, Shen, Hui, Weisenberger, Daniel J, Bootwalla, Moiz, Baylin, Stephen B, Laird, Peter W, Cherniack, Andrew D, Saksena, Gordon, Haake, Scott, Li, Jun, Liang, Han, Lu, Yiling, Mills, Gordon B, Akbani, Rehan, Leiserson, Mark DM, Raphael, Benjamin J, Anur, Pavana, Bottaro, Donald, Albiges, Laurence, Barnabas, Nandita, Choueiri, Toni K, Czerniak, Bogdan, Godwin, Andrew K, Hakimi, A Ari, Ho, Thai H, Hsieh, James, Ittmann, Michael, Kim, William Y, Krishnan, Bhavani, Merino, Maria J, Mills Shaw, Kenna R, Reuter, Victor E, Reznik, Ed, Shelley, Carl S, Shuch, Brian, Signoretti, Sabina, Srinivasan, Ramaprasad, Tamboli, Pheroze, Thomas, George, Tickoo, Satish, Burnett, Kenneth, Crain, Daniel, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph D, Penny, Robert J, Shelton, Candace, Shelton, W Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Avedon, Melissa T, Bowen, Jay, Gastier-Foster, Julie M, Gerken, Mark, Leraas, Kristen M, Lichtenberg, Tara M, Ramirez, Nilsa C, Santos, Tracie, Wise, Lisa, Zmuda, Erik, Demchok, John A, Felau, Ina, Hutter, Carolyn M, Sheth, Margi, Sofia, Heidi J, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C, Zhang, Jiashan, Ayala, Brenda, Baboud, Julien, Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Cancer Genome Atlas Research Network, Cancer Genome Atlas Research Network, Linehan, W Marston, Spellman, Paul T, Ricketts, Christopher J, Creighton, Chad J, Fei, Suzanne S, Davis, Caleb, Wheeler, David A, Murray, Bradley A, Schmidt, Laura, Vocke, Cathy D, Peto, Myron, Al Mamun, Abu Amar M, Shinbrot, Eve, Sethi, Anurag, Brooks, Samira, Rathmell, W Kimryn, Brooks, Angela N, Hoadley, Katherine A, Robertson, A Gordon, Brooks, Denise, Bowlby, Reanne, Sadeghi, Sara, Shen, Hui, Weisenberger, Daniel J, Bootwalla, Moiz, Baylin, Stephen B, Laird, Peter W, Cherniack, Andrew D, Saksena, Gordon, Haake, Scott, Li, Jun, Liang, Han, Lu, Yiling, Mills, Gordon B, Akbani, Rehan, Leiserson, Mark DM, Raphael, Benjamin J, Anur, Pavana, Bottaro, Donald, Albiges, Laurence, Barnabas, Nandita, Choueiri, Toni K, Czerniak, Bogdan, Godwin, Andrew K, Hakimi, A Ari, Ho, Thai H, Hsieh, James, Ittmann, Michael, Kim, William Y, Krishnan, Bhavani, Merino, Maria J, Mills Shaw, Kenna R, Reuter, Victor E, Reznik, Ed, Shelley, Carl S, Shuch, Brian, Signoretti, Sabina, Srinivasan, Ramaprasad, Tamboli, Pheroze, Thomas, George, Tickoo, Satish, Burnett, Kenneth, Crain, Daniel, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph D, Penny, Robert J, Shelton, Candace, Shelton, W Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Avedon, Melissa T, Bowen, Jay, Gastier-Foster, Julie M, Gerken, Mark, Leraas, Kristen M, Lichtenberg, Tara M, Ramirez, Nilsa C, Santos, Tracie, Wise, Lisa, Zmuda, Erik, Demchok, John A, Felau, Ina, Hutter, Carolyn M, Sheth, Margi, Sofia, Heidi J, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C, Zhang, Jiashan, Ayala, Brenda, Baboud, Julien, Chudamani, Sudha, Liu, Jia, and Lolla, Laxmi

Abstract

BackgroundPapillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist.MethodsWe performed comprehensive molecular characterization of 161 primary papillary renal-cell carcinomas, using whole-exome sequencing, copy-number analysis, messenger RNA and microRNA sequencing, DNA-methylation analysis, and proteomic analysis.ResultsType 1 and type 2 papillary renal-cell carcinomas were shown to be different types of renal cancer characterized by specific genetic alterations, with type 2 further classified into three individual subgroups on the basis of molecular differences associated with patient survival. Type 1 tumors were associated with MET alterations, whereas type 2 tumors were characterized by CDKN2A silencing, SETD2 mutations, TFE3 fusions, and increased expression of the NRF2-antioxidant response element (ARE) pathway. A CpG island methylator phenotype (CIMP) was observed in a distinct subgroup of type 2 papillary renal-cell carcinomas that was characterized by poor survival and mutation of the gene encoding fumarate hydratase (FH).ConclusionsType 1 and type 2 papillary renal-cell carcinomas were shown to be clinically and biologically distinct. Alterations in the MET pathway were associated with type 1, and activation of the NRF2-ARE pathway was associated with type 2; CDKN2A loss and CIMP in type 2 conveyed a poor prognosis. Furthermore, type 2 papillary renal-cell carcinoma consisted of at least three subtypes based on molecular and phenotypic features. (Funded by the National Institutes of Health.).

Published
2016

38. Whole-Exome Sequencing in Two Extreme Phenotypes of Response to VEGF-Targeted Therapies in Patients With Metastatic Clear Cell Renal Cell Carcinoma

Author

Fay, Andre P., primary, de Velasco, Guillermo, additional, Ho, Thai H., additional, Van Allen, Eliezer M., additional, Murray, Bradley, additional, Albiges, Laurence, additional, Signoretti, Sabina, additional, Hakimi, A. Ari, additional, Stanton, Melissa L., additional, Bellmunt, Joaquim, additional, McDermott, David F., additional, Atkins, Michael B., additional, Garraway, Levi A., additional, Kwiatkowski, David J., additional, and Choueiri, Toni K., additional

Published
2016
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39. Integrated genomic correlates of response to PD-1 inhibitor nivolumab in metastatic renal cell carcinoma (mRCC).

Author

de Velasco, Guillermo, primary, Miao, Diana, additional, Shukla, Sachet, additional, Voss, Martin Henner, additional, Wu, Catherine, additional, Murray, Bradley, additional, Meyerson, Matthew, additional, Signoretti, Sabina, additional, Motzer, Robert J., additional, Van Allen, Eliezer Mendel, additional, and Choueiri, Toni K., additional

Published
2016
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41. GENO-06A PAN-GLIOMA CHARACTERIZATION OF GENOMIC, EPIGENOMIC AND TRANSCRIPTOMIC ACTIVITIES REVEALS NOVEL RELATIONSHIPS BETWEEN HISTOLOGICAL SUBTYPES AND MOLECULAR SIGNATURES

Author

Barthel, Floris P., primary, Ceccarelli, Michele, additional, Malta, Tathiane M., additional, Sabedot, Thais S., additional, Salama, Sofie R., additional, Pagnotta, Stefano M., additional, Murray, Bradley A., additional, Morozova, Olena, additional, Newton, Yulia, additional, Brat, Daniel J., additional, Cherniack, Andrew D., additional, Zhang, Hailei, additional, Poisson, Laila, additional, Cooper, Lee, additional, Rabadan, Raul, additional, Laird, Peter W., additional, Gutmann, David H., additional, Noushmehr, Houtan, additional, Iavarone, Antonio, additional, and Verhaak, Roel G.W., additional

Published
2015
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42. The Molecular Taxonomy of Primary Prostate Cancer

Author

Abeshouse, Adam, primary, Ahn, Jaeil, additional, Akbani, Rehan, additional, Ally, Adrian, additional, Amin, Samirkumar, additional, Andry, Christopher D., additional, Annala, Matti, additional, Aprikian, Armen, additional, Armenia, Joshua, additional, Arora, Arshi, additional, Auman, J. Todd, additional, Balasundaram, Miruna, additional, Balu, Saianand, additional, Barbieri, Christopher E., additional, Bauer, Thomas, additional, Benz, Christopher C., additional, Bergeron, Alain, additional, Beroukhim, Rameen, additional, Berrios, Mario, additional, Bivol, Adrian, additional, Bodenheimer, Tom, additional, Boice, Lori, additional, Bootwalla, Moiz S., additional, Borges dos Reis, Rodolfo, additional, Boutros, Paul C., additional, Bowen, Jay, additional, Bowlby, Reanne, additional, Boyd, Jeffrey, additional, Bradley, Robert K., additional, Breggia, Anne, additional, Brimo, Fadi, additional, Bristow, Christopher A., additional, Brooks, Denise, additional, Broom, Bradley M., additional, Bryce, Alan H., additional, Bubley, Glenn, additional, Burks, Eric, additional, Butterfield, Yaron S.N., additional, Button, Michael, additional, Canes, David, additional, Carlotti, Carlos G., additional, Carlsen, Rebecca, additional, Carmel, Michel, additional, Carroll, Peter R., additional, Carter, Scott L., additional, Cartun, Richard, additional, Carver, Brett S., additional, Chan, June M., additional, Chang, Matthew T., additional, Chen, Yu, additional, Cherniack, Andrew D., additional, Chevalier, Simone, additional, Chin, Lynda, additional, Cho, Juok, additional, Chu, Andy, additional, Chuah, Eric, additional, Chudamani, Sudha, additional, Cibulskis, Kristian, additional, Ciriello, Giovanni, additional, Clarke, Amanda, additional, Cooperberg, Matthew R., additional, Corcoran, Niall M., additional, Costello, Anthony J., additional, Cowan, Janet, additional, Crain, Daniel, additional, Curley, Erin, additional, David, Kerstin, additional, Demchok, John A., additional, Demichelis, Francesca, additional, Dhalla, Noreen, additional, Dhir, Rajiv, additional, Doueik, Alexandre, additional, Drake, Bettina, additional, Dvinge, Heidi, additional, Dyakova, Natalya, additional, Felau, Ina, additional, Ferguson, Martin L., additional, Frazer, Scott, additional, Freedland, Stephen, additional, Fu, Yao, additional, Gabriel, Stacey B., additional, Gao, Jianjiong, additional, Gardner, Johanna, additional, Gastier-Foster, Julie M., additional, Gehlenborg, Nils, additional, Gerken, Mark, additional, Gerstein, Mark B., additional, Getz, Gad, additional, Godwin, Andrew K., additional, Gopalan, Anuradha, additional, Graefen, Markus, additional, Graim, Kiley, additional, Gribbin, Thomas, additional, Guin, Ranabir, additional, Gupta, Manaswi, additional, Hadjipanayis, Angela, additional, Haider, Syed, additional, Hamel, Lucie, additional, Hayes, D. Neil, additional, Heiman, David I., additional, Hess, Julian, additional, Hoadley, Katherine A., additional, Holbrook, Andrea H., additional, Holt, Robert A., additional, Holway, Antonia, additional, Hovens, Christopher M., additional, Hoyle, Alan P., additional, Huang, Mei, additional, Hutter, Carolyn M., additional, Ittmann, Michael, additional, Iype, Lisa, additional, Jefferys, Stuart R., additional, Jones, Corbin D., additional, Jones, Steven J.M., additional, Juhl, Hartmut, additional, Kahles, Andre, additional, Kane, Christopher J., additional, Kasaian, Katayoon, additional, Kerger, Michael, additional, Khurana, Ekta, additional, Kim, Jaegil, additional, Klein, Robert J., additional, Kucherlapati, Raju, additional, Lacombe, Louis, additional, Ladanyi, Marc, additional, Lai, Phillip H., additional, Laird, Peter W., additional, Lander, Eric S., additional, Latour, Mathieu, additional, Lawrence, Michael S., additional, Lau, Kevin, additional, LeBien, Tucker, additional, Lee, Darlene, additional, Lee, Semin, additional, Lehmann, Kjong-Van, additional, Leraas, Kristen M., additional, Leshchiner, Ignaty, additional, Leung, Robert, additional, Libertino, John A., additional, Lichtenberg, Tara M., additional, Lin, Pei, additional, Linehan, W. Marston, additional, Ling, Shiyun, additional, Lippman, Scott M., additional, Liu, Jia, additional, Liu, Wenbin, additional, Lochovsky, Lucas, additional, Loda, Massimo, additional, Logothetis, Christopher, additional, Lolla, Laxmi, additional, Longacre, Teri, additional, Lu, Yiling, additional, Luo, Jianhua, additional, Ma, Yussanne, additional, Mahadeshwar, Harshad S., additional, Mallery, David, additional, Mariamidze, Armaz, additional, Marra, Marco A., additional, Mayo, Michael, additional, McCall, Shannon, additional, McKercher, Ginette, additional, Meng, Shaowu, additional, Mes-Masson, Anne-Marie, additional, Merino, Maria J., additional, Meyerson, Matthew, additional, Mieczkowski, Piotr A., additional, Mills, Gordon B., additional, Shaw, Kenna R. Mills, additional, Minner, Sarah, additional, Moinzadeh, Alireza, additional, Moore, Richard A., additional, Morris, Scott, additional, Morrison, Carl, additional, Mose, Lisle E., additional, Mungall, Andrew J., additional, Murray, Bradley A., additional, Myers, Jerome B., additional, Naresh, Rashi, additional, Nelson, Joel, additional, Nelson, Mark A., additional, Nelson, Peter S., additional, Newton, Yulia, additional, Noble, Michael S., additional, Noushmehr, Houtan, additional, Nykter, Matti, additional, Pantazi, Angeliki, additional, Parfenov, Michael, additional, Park, Peter J., additional, Parker, Joel S., additional, Paulauskis, Joseph, additional, Penny, Robert, additional, Perou, Charles M., additional, Piché, Alain, additional, Pihl, Todd, additional, Pinto, Peter A., additional, Prandi, Davide, additional, Protopopov, Alexei, additional, Ramirez, Nilsa C., additional, Rao, Arvind, additional, Rathmell, W. Kimryn, additional, Rätsch, Gunnar, additional, Ren, Xiaojia, additional, Reuter, Victor E., additional, Reynolds, Sheila M., additional, Rhie, Suhn K., additional, Rieger-Christ, Kimberly, additional, Roach, Jeffrey, additional, Robertson, A. Gordon, additional, Robinson, Brian, additional, Rubin, Mark A., additional, Saad, Fred, additional, Sadeghi, Sara, additional, Saksena, Gordon, additional, Saller, Charles, additional, Salner, Andrew, additional, Sanchez-Vega, Francisco, additional, Sander, Chris, additional, Sandusky, George, additional, Sauter, Guido, additional, Sboner, Andrea, additional, Scardino, Peter T., additional, Scarlata, Eleonora, additional, Schein, Jacqueline E., additional, Schlomm, Thorsten, additional, Schmidt, Laura S., additional, Schultz, Nikolaus, additional, Schumacher, Steven E., additional, Seidman, Jonathan, additional, Neder, Luciano, additional, Seth, Sahil, additional, Sharp, Alexis, additional, Shelton, Candace, additional, Shelton, Troy, additional, Shen, Hui, additional, Shen, Ronglai, additional, Sherman, Mark, additional, Sheth, Margi, additional, Shi, Yan, additional, Shih, Juliann, additional, Shmulevich, Ilya, additional, Simko, Jeffry, additional, Simon, Ronald, additional, Simons, Janae V., additional, Sipahimalani, Payal, additional, Skelly, Tara, additional, Sofia, Heidi J., additional, Soloway, Matthew G., additional, Song, Xingzhi, additional, Sorcini, Andrea, additional, Sougnez, Carrie, additional, Stepa, Serghei, additional, Stewart, Chip, additional, Stewart, John, additional, Stuart, Joshua M., additional, Sullivan, Travis B., additional, Sun, Charlie, additional, Sun, Huandong, additional, Tam, Angela, additional, Tan, Donghui, additional, Tang, Jiabin, additional, Tarnuzzer, Roy, additional, Tarvin, Katherine, additional, Taylor, Barry S., additional, Teebagy, Patrick, additional, Tenggara, Imelda, additional, Têtu, Bernard, additional, Tewari, Ashutosh, additional, Thiessen, Nina, additional, Thompson, Timothy, additional, Thorne, Leigh B., additional, Tirapelli, Daniela P., additional, Tomlins, Scott A., additional, Trevisan, Felipe Amstalden, additional, Troncoso, Patricia, additional, True, Lawrence D., additional, Tsourlakis, Maria Christina, additional, Tyekucheva, Svitlana, additional, Van Allen, Eliezer, additional, Van Den Berg, David J., additional, Veluvolu, Umadevi, additional, Verhaak, Roel, additional, Vocke, Cathy D., additional, Voet, Doug, additional, Wan, Yunhu, additional, Wang, Qingguo, additional, Wang, Wenyi, additional, Wang, Zhining, additional, Weinhold, Nils, additional, Weinstein, John N., additional, Weisenberger, Daniel J., additional, Wilkerson, Matthew D., additional, Wise, Lisa, additional, Witte, John, additional, Wu, Chia-Chin, additional, Wu, Junyuan, additional, Wu, Ye, additional, Xu, Andrew W., additional, Yadav, Shalini S., additional, Yang, Liming, additional, Yang, Lixing, additional, Yau, Christina, additional, Ye, Huihui, additional, Yena, Peggy, additional, Zeng, Thomas, additional, Zenklusen, Jean C., additional, Zhang, Hailei, additional, Zhang, Jianhua, additional, Zhang, Jiashan, additional, Zhang, Wei, additional, Zhong, Yi, additional, Zhu, Kelsey, additional, and Zmuda, Erik, additional

Published
2015
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43. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer

Author

Ciriello, Giovanni, primary, Gatza, Michael L., additional, Beck, Andrew H., additional, Wilkerson, Matthew D., additional, Rhie, Suhn K., additional, Pastore, Alessandro, additional, Zhang, Hailei, additional, McLellan, Michael, additional, Yau, Christina, additional, Kandoth, Cyriac, additional, Bowlby, Reanne, additional, Shen, Hui, additional, Hayat, Sikander, additional, Fieldhouse, Robert, additional, Lester, Susan C., additional, Tse, Gary M.K., additional, Factor, Rachel E., additional, Collins, Laura C., additional, Allison, Kimberly H., additional, Chen, Yunn-Yi, additional, Jensen, Kristin, additional, Johnson, Nicole B., additional, Oesterreich, Steffi, additional, Mills, Gordon B., additional, Cherniack, Andrew D., additional, Robertson, Gordon, additional, Benz, Christopher, additional, Sander, Chris, additional, Laird, Peter W., additional, Hoadley, Katherine A., additional, King, Tari A., additional, Perou, Charles M., additional, Akbani, Rehan, additional, Auman, J. Todd, additional, Balasundaram, Miruna, additional, Balu, Saianand, additional, Barr, Thomas, additional, Beck, Andrew, additional, Benz, Stephen, additional, Berrios, Mario, additional, Beroukhim, Rameen, additional, Bodenheimer, Tom, additional, Boice, Lori, additional, Bootwalla, Moiz S., additional, Bowen, Jay, additional, Brooks, Denise, additional, Chin, Lynda, additional, Cho, Juok, additional, Chudamani, Sudha, additional, Ciriello, Giovanni, additional, Davidsen, Tanja, additional, Demchok, John A., additional, Dennison, Jennifer B., additional, Ding, Li, additional, Felau, Ina, additional, Ferguson, Martin L., additional, Frazer, Scott, additional, Gabriel, Stacey B., additional, Gao, JianJiong, additional, Gastier-Foster, Julie M., additional, Gehlenborg, Nils, additional, Gerken, Mark, additional, Getz, Gad, additional, Gibson, William J., additional, Hayes, D. Neil, additional, Heiman, David I., additional, Holbrook, Andrea, additional, Holt, Robert A., additional, Hoyle, Alan P., additional, Hu, Hai, additional, Huang, Mei, additional, Hutter, Carolyn M., additional, Hwang, E. Shelley, additional, Jefferys, Stuart R., additional, Jones, Steven J.M., additional, Ju, Zhenlin, additional, Kim, Jaegil, additional, Lai, Phillip H., additional, Lawrence, Michael S., additional, Leraas, Kristen M., additional, Lichtenberg, Tara M., additional, Lin, Pei, additional, Ling, Shiyun, additional, Liu, Jia, additional, Liu, Wenbin, additional, Lolla, Laxmi, additional, Lu, Yiling, additional, Ma, Yussanne, additional, Maglinte, Dennis T., additional, Mardis, Elaine, additional, Marks, Jeffrey, additional, Marra, Marco A., additional, McAllister, Cynthia, additional, Meng, Shaowu, additional, Meyerson, Matthew, additional, Moore, Richard A., additional, Mose, Lisle E., additional, Mungall, Andrew J., additional, Murray, Bradley A., additional, Naresh, Rashi, additional, Noble, Michael S., additional, Olopade, Olufunmilayo, additional, Parker, Joel S., additional, Perou, Charles M., additional, Pihl, Todd, additional, Saksena, Gordon, additional, Schumacher, Steven E., additional, Shaw, Kenna R. Mills, additional, Ramirez, Nilsa C., additional, Rathmell, W. Kimryn, additional, Roach, Jeffrey, additional, Robertson, A. Gordon, additional, Schein, Jacqueline E., additional, Schultz, Nikolaus, additional, Sheth, Margi, additional, Shi, Yan, additional, Shih, Juliann, additional, Shelley, Carl Simon, additional, Shriver, Craig, additional, Simons, Janae V., additional, Sofia, Heidi J., additional, Soloway, Matthew G., additional, Sougnez, Carrie, additional, Sun, Charlie, additional, Tarnuzzer, Roy, additional, Tiezzi, Daniel G., additional, Van Den Berg, David J., additional, Voet, Doug, additional, Wan, Yunhu, additional, Wang, Zhining, additional, Weinstein, John N., additional, Weisenberger, Daniel J., additional, Wilson, Richard, additional, Wise, Lisa, additional, Wiznerowicz, Maciej, additional, Wu, Junyuan, additional, Wu, Ye, additional, Yang, Liming, additional, Zack, Travis I., additional, Zenklusen, Jean C., additional, Zhang, Jiashan, additional, and Zmuda, Erik, additional

Published
2015
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44. Structure and mechanism of activity-based inhibition of the EGF receptor by Mig6

Author

Park, Eunyoung, primary, Kim, Nayoung, additional, Ficarro, Scott B, additional, Zhang, Yi, additional, Lee, Byung Il, additional, Cho, Ahye, additional, Kim, Kihong, additional, Park, Angela K J, additional, Park, Woong-Yang, additional, Murray, Bradley, additional, Meyerson, Matthew, additional, Beroukhim, Rameen, additional, Marto, Jarrod A, additional, Cho, Jeonghee, additional, and Eck, Michael J, additional

Published
2015
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46. Genomic Classification of Cutaneous Melanoma

Author

Akbani, Rehan, primary, Akdemir, Kadir C., additional, Aksoy, B. Arman, additional, Albert, Monique, additional, Ally, Adrian, additional, Amin, Samirkumar B., additional, Arachchi, Harindra, additional, Arora, Arshi, additional, Auman, J. Todd, additional, Ayala, Brenda, additional, Baboud, Julien, additional, Balasundaram, Miruna, additional, Balu, Saianand, additional, Barnabas, Nandita, additional, Bartlett, John, additional, Bartlett, Pam, additional, Bastian, Boris C., additional, Baylin, Stephen B., additional, Behera, Madhusmita, additional, Belyaev, Dmitry, additional, Benz, Christopher, additional, Bernard, Brady, additional, Beroukhim, Rameen, additional, Bir, Natalie, additional, Black, Aaron D., additional, Bodenheimer, Tom, additional, Boice, Lori, additional, Boland, Genevieve M., additional, Bono, Riccardo, additional, Bootwalla, Moiz S., additional, Bosenberg, Marcus, additional, Bowen, Jay, additional, Bowlby, Reanne, additional, Bristow, Christopher A., additional, Brockway-Lunardi, Laura, additional, Brooks, Denise, additional, Brzezinski, Jakub, additional, Bshara, Wiam, additional, Buda, Elizabeth, additional, Burns, William R., additional, Butterfield, Yaron S.N., additional, Button, Michael, additional, Calderone, Tiffany, additional, Cappellini, Giancarlo Antonini, additional, Carter, Candace, additional, Carter, Scott L., additional, Cherney, Lynn, additional, Cherniack, Andrew D., additional, Chevalier, Aaron, additional, Chin, Lynda, additional, Cho, Juok, additional, Cho, Raymond J., additional, Choi, Yoon-La, additional, Chu, Andy, additional, Chudamani, Sudha, additional, Cibulskis, Kristian, additional, Ciriello, Giovanni, additional, Clarke, Amanda, additional, Coons, Stephen, additional, Cope, Leslie, additional, Crain, Daniel, additional, Curley, Erin, additional, Danilova, Ludmila, additional, D’Atri, Stefania, additional, Davidsen, Tanja, additional, Davies, Michael A., additional, Delman, Keith A., additional, Demchok, John A., additional, Deng, Qixia A., additional, Deribe, Yonathan Lissanu, additional, Dhalla, Noreen, additional, Dhir, Rajiv, additional, DiCara, Daniel, additional, Dinikin, Michael, additional, Dubina, Michael, additional, Ebrom, J. Stephen, additional, Egea, Sophie, additional, Eley, Greg, additional, Engel, Jay, additional, Eschbacher, Jennifer M., additional, Fedosenko, Konstantin V., additional, Felau, Ina, additional, Fennell, Timothy, additional, Ferguson, Martin L., additional, Fisher, Sheila, additional, Flaherty, Keith T., additional, Frazer, Scott, additional, Frick, Jessica, additional, Fulidou, Victoria, additional, Gabriel, Stacey B., additional, Gao, Jianjiong, additional, Gardner, Johanna, additional, Garraway, Levi A., additional, Gastier-Foster, Julie M., additional, Gaudioso, Carmelo, additional, Gehlenborg, Nils, additional, Genovese, Giannicola, additional, Gerken, Mark, additional, Gershenwald, Jeffrey E., additional, Getz, Gad, additional, Gomez-Fernandez, Carmen, additional, Gribbin, Thomas, additional, Grimsby, Jonna, additional, Gross, Benjamin, additional, Guin, Ranabir, additional, Gutschner, Tony, additional, Hadjipanayis, Angela, additional, Halaban, Ruth, additional, Hanf, Benjamin, additional, Haussler, David, additional, Haydu, Lauren E., additional, Hayes, D. Neil, additional, Hayward, Nicholas K., additional, Heiman, David I., additional, Herbert, Lynn, additional, Herman, James G., additional, Hersey, Peter, additional, Hoadley, Katherine A., additional, Hodis, Eran, additional, Holt, Robert A., additional, Hoon, Dave SB., additional, Hoppough, Susan, additional, Hoyle, Alan P., additional, Huang, Franklin W., additional, Huang, Mei, additional, Huang, Sharon, additional, Hutter, Carolyn M., additional, Ibbs, Matthew, additional, Iype, Lisa, additional, Jacobsen, Anders, additional, Jakrot, Valerie, additional, Janning, Alyssa, additional, Jeck, William R., additional, Jefferys, Stuart R., additional, Jensen, Mark A., additional, Jones, Corbin D., additional, Jones, Steven J.M., additional, Ju, Zhenlin, additional, Kakavand, Hojabr, additional, Kang, Hyojin, additional, Kefford, Richard F., additional, Khuri, Fadlo R., additional, Kim, Jaegil, additional, Kirkwood, John M., additional, Klode, Joachim, additional, Korkut, Anil, additional, Korski, Konstanty, additional, Krauthammer, Michael, additional, Kucherlapati, Raju, additional, Kwong, Lawrence N., additional, Kycler, Witold, additional, Ladanyi, Marc, additional, Lai, Phillip H., additional, Laird, Peter W., additional, Lander, Eric, additional, Lawrence, Michael S., additional, Lazar, Alexander J., additional, Łaźniak, Radoslaw, additional, Lee, Darlene, additional, Lee, Jeffrey E., additional, Lee, Junehawk, additional, Lee, Kenneth, additional, Lee, Semin, additional, Lee, William, additional, Leporowska, Ewa, additional, Leraas, Kristen M., additional, Li, Haiyan I., additional, Lichtenberg, Tara M., additional, Lichtenstein, Lee, additional, Lin, Pei, additional, Ling, Shiyun, additional, Liu, Jia, additional, Liu, Ouida, additional, Liu, Wenbin, additional, Long, Georgina V., additional, Lu, Yiling, additional, Ma, Singer, additional, Ma, Yussanne, additional, Mackiewicz, Andrzej, additional, Mahadeshwar, Harshad S., additional, Malke, Jared, additional, Mallery, David, additional, Manikhas, Georgy M., additional, Mann, Graham J., additional, Marra, Marco A., additional, Matejka, Brenna, additional, Mayo, Michael, additional, Mehrabi, Sousan, additional, Meng, Shaowu, additional, Meyerson, Matthew, additional, Mieczkowski, Piotr A., additional, Miller, John P., additional, Miller, Martin L., additional, Mills, Gordon B., additional, Moiseenko, Fedor, additional, Moore, Richard A., additional, Morris, Scott, additional, Morrison, Carl, additional, Morton, Donald, additional, Moschos, Stergios, additional, Mose, Lisle E., additional, Muller, Florian L., additional, Mungall, Andrew J., additional, Murawa, Dawid, additional, Murawa, Pawel, additional, Murray, Bradley A., additional, Nezi, Luigi, additional, Ng, Sam, additional, Nicholson, Dana, additional, Noble, Michael S., additional, Osunkoya, Adeboye, additional, Owonikoko, Taofeek K., additional, Ozenberger, Bradley A., additional, Pagani, Elena, additional, Paklina, Oxana V., additional, Pantazi, Angeliki, additional, Parfenov, Michael, additional, Parfitt, Jeremy, additional, Park, Peter J., additional, Park, Woong-Yang, additional, Parker, Joel S., additional, Passarelli, Francesca, additional, Penny, Robert, additional, Perou, Charles M., additional, Pihl, Todd D., additional, Potapova, Olga, additional, Prieto, Victor G., additional, Protopopov, Alexei, additional, Quinn, Michael J., additional, Radenbaugh, Amie, additional, Rai, Kunal, additional, Ramalingam, Suresh S., additional, Raman, Ayush T., additional, Ramirez, Nilsa C., additional, Ramirez, Ricardo, additional, Rao, Uma, additional, Rathmell, W. Kimryn, additional, Ren, Xiaojia, additional, Reynolds, Sheila M., additional, Roach, Jeffrey, additional, Robertson, A. Gordon, additional, Ross, Merrick I., additional, Roszik, Jason, additional, Russo, Giandomenico, additional, Saksena, Gordon, additional, Saller, Charles, additional, Samuels, Yardena, additional, Sander, Chris, additional, Sander, Cindy, additional, Sandusky, George, additional, Santoso, Netty, additional, Saul, Melissa, additional, Saw, Robyn PM., additional, Schadendorf, Dirk, additional, Schein, Jacqueline E., additional, Schultz, Nikolaus, additional, Schumacher, Steven E., additional, Schwallier, Charles, additional, Scolyer, Richard A., additional, Seidman, Jonathan, additional, Sekhar, Pedamallu Chandra, additional, Sekhon, Harmanjatinder S., additional, Senbabaoglu, Yasin, additional, Seth, Sahil, additional, Shannon, Kerwin F., additional, Sharpe, Samantha, additional, Sharpless, Norman E., additional, Shaw, Kenna R. Mills, additional, Shelton, Candace, additional, Shelton, Troy, additional, Shen, Ronglai, additional, Sheth, Margi, additional, Shi, Yan, additional, Shiau, Carolyn J., additional, Shmulevich, Ilya, additional, Sica, Gabriel L., additional, Simons, Janae V., additional, Sinha, Rileen, additional, Sipahimalani, Payal, additional, Sofia, Heidi J., additional, Soloway, Matthew G., additional, Song, Xingzhi, additional, Sougnez, Carrie, additional, Spillane, Andrew J., additional, Spychała, Arkadiusz, additional, Stretch, Jonathan R., additional, Stuart, Joshua, additional, Suchorska, Wiktoria M., additional, Sucker, Antje, additional, Sumer, S. Onur, additional, Sun, Yichao, additional, Synott, Maria, additional, Tabak, Barbara, additional, Tabler, Teresa R., additional, Tam, Angela, additional, Tan, Donghui, additional, Tang, Jiabin, additional, Tarnuzzer, Roy, additional, Tarvin, Katherine, additional, Tatka, Honorata, additional, Taylor, Barry S., additional, Teresiak, Marek, additional, Thiessen, Nina, additional, Thompson, John F., additional, Thorne, Leigh, additional, Thorsson, Vesteinn, additional, Trent, Jeffrey M., additional, Triche, Timothy J., additional, Tsai, Kenneth Y., additional, Tsou, Peiling, additional, Van Den Berg, David J., additional, Van Allen, Eliezer M., additional, Veluvolu, Umadevi, additional, Verhaak, Roeland G., additional, Voet, Douglas, additional, Voronina, Olga, additional, Walter, Vonn, additional, Walton, Jessica S., additional, Wan, Yunhu, additional, Wang, Yuling, additional, Wang, Zhining, additional, Waring, Scot, additional, Watson, Ian R., additional, Weinhold, Nils, additional, Weinstein, John N., additional, Weisenberger, Daniel J., additional, White, Peter, additional, Wilkerson, Matthew D., additional, Wilmott, James S., additional, Wise, Lisa, additional, Wiznerowicz, Maciej, additional, Woodman, Scott E., additional, Wu, Chang-Jiun, additional, Wu, Chia-Chin, additional, Wu, Junyuan, additional, Wu, Ye, additional, Xi, Ruibin, additional, Xu, Andrew Wei, additional, Yang, Da, additional, Yang, Liming, additional, Yang, Lixing, additional, Zack, Travis I., additional, Zenklusen, Jean C., additional, Zhang, Hailei, additional, Zhang, Jianhua, additional, Zhang, Wei, additional, Zhao, Xiaobei, additional, Zhu, Jingchun, additional, Zhu, Kelsey, additional, Zimmer, Lisa, additional, Zmuda, Erik, additional, and Zou, Lihua, additional

Published
2015
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48. Whole-exome sequencing (WES) predicting two extreme phenotypes of response to VEGF-targeted therapies (VEGF-TT) in patients with metastatic clear cell renal cell carcinoma (mRCC).

Author

Fay, Andre Poisl, primary, Van Allen, Eliezer Mendel, additional, Murray, Bradley, additional, Albiges, Laurence, additional, Signoretti, Sabina, additional, Ho, Thai Huu, additional, Hakimi, A. Ari, additional, Mickey, Suzanne S, additional, Stanton, Melissa L., additional, Bellmunt, Joaquim, additional, McDermott, David F., additional, Atkins, Michael B., additional, Garraway, Levi A., additional, Kwiatkowski, David J., additional, and Choueiri, Toni K., additional

Published
2015
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50. Abstract 4692: Relationships between somatic genomic alterations, tumor stage and progression-free survival in cervical cancer

Author

Ojesina, Akinyemi I., primary, Murray, Bradley, additional, Bjorge, Line, additional, Woie, Kathrine, additional, Krakstad, Camilla, additional, Lichtenstein, Lee, additional, Pedamallu, Chandra Sekhar, additional, Taylor-Weiner, Amaro, additional, Freeman, Samuel S., additional, Cherniack, Andrew D., additional, Lawrence, Michael S., additional, Cibulskis, Kristian, additional, Carter, Scott L., additional, Walline, Heather, additional, Carey, Thomas E., additional, Vintermyr, Olav K., additional, Bertelsen, Bjorn, additional, Crum, Christopher P., additional, Getz, Gad, additional, Meyerson, Matthew, additional, and Salvesen, Helga B., additional

Published
2014
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