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153 results on '"Zenklusen, Jean Claude"'

1. Integrative Molecular Characterization of Malignant Pleural Mesothelioma

Author

Hmeljak, Julija, Sanchez-Vega, Francisco, Hoadley, Katherine A, Shih, Juliann, Stewart, Chip, Heiman, David, Tarpey, Patrick, Danilova, Ludmila, Drill, Esther, Gibb, Ewan A, Bowlby, Reanne, Kanchi, Rupa, Osmanbeyoglu, Hatice U, Sekido, Yoshitaka, Takeshita, Jumpei, Newton, Yulia, Graim, Kiley, Gupta, Manaswi, Gay, Carl M, Diao, Lixia, Gibbs, David L, Thorsson, Vesteinn, Iype, Lisa, Kantheti, Havish, Severson, David T, Ravegnini, Gloria, Desmeules, Patrice, Jungbluth, Achim A, Travis, William D, Dacic, Sanja, Chirieac, Lucian R, Galateau-Sallé, Françoise, Fujimoto, Junya, Husain, Aliya N, Silveira, Henrique C, Rusch, Valerie W, Rintoul, Robert C, Pass, Harvey, Kindler, Hedy, Zauderer, Marjorie G, Kwiatkowski, David J, Bueno, Raphael, Tsao, Anne S, Creaney, Jenette, Lichtenberg, Tara, Leraas, Kristen, Bowen, Jay, Felau, Ina, Zenklusen, Jean Claude, Akbani, Rehan, Cherniack, Andrew D, Byers, Lauren A, Noble, Michael S, Fletcher, Jonathan A, Robertson, A Gordon, Shen, Ronglai, Aburatani, Hiroyuki, Robinson, Bruce W, Campbell, Peter, Ladanyi, Marc, Ally, Adrian, Anur, Pavana, Armenia, Joshua, Auman, J Todd, Balasundaram, Miruna, Balu, Saianand, Baylin, Stephen B, Becich, Michael, Behrens, Carmen, Beroukhim, Rameen, Bielski, Craig, Bodenheimer, Tom, Bootwalla, Moiz S, Brooks, Denise, Byers, Lauren Averett, Cárcano, Flávio M, Carlsen, Rebecca, Carvalho, Andre L, Cheung, Dorothy, Chirieac, Lucian, Cho, Juok, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cope, Leslie, Crain, Daniel, Curley, Erin, Rienzo, Assunta De, DeFreitas, Timothy, Demchok, John A, and Dhalla, Noreen

Subjects
Rare Diseases, Lung Cancer, Biotechnology, Lung, Cancer, Human Genome, Genetics, 2.1 Biological and endogenous factors, Aetiology, Good Health and Well Being, Aged, Biomarkers, Tumor, Female, Histone-Lysine N-Methyltransferase, Humans, Kaplan-Meier Estimate, Lung Neoplasms, Male, Mesothelioma, Middle Aged, Mutation, Pleural Neoplasms, Prognosis, Protein Methyltransferases, Tumor Suppressor Proteins, Ubiquitin Thiolesterase, TCGA Research Network, Oncology and Carcinogenesis
Abstract

Malignant pleural mesothelioma (MPM) is a highly lethal cancer of the lining of the chest cavity. To expand our understanding of MPM, we conducted a comprehensive integrated genomic study, including the most detailed analysis of BAP1 alterations to date. We identified histology-independent molecular prognostic subsets, and defined a novel genomic subtype with TP53 and SETDB1 mutations and extensive loss of heterozygosity. We also report strong expression of the immune-checkpoint gene VISTA in epithelioid MPM, strikingly higher than in other solid cancers, with implications for the immune response to MPM and for its immunotherapy. Our findings highlight new avenues for further investigation of MPM biology and novel therapeutic options. SIGNIFICANCE: Through a comprehensive integrated genomic study of 74 MPMs, we provide a deeper understanding of histology-independent determinants of aggressive behavior, define a novel genomic subtype with TP53 and SETDB1 mutations and extensive loss of heterozygosity, and discovered strong expression of the immune-checkpoint gene VISTA in epithelioid MPM.See related commentary by Aggarwal and Albelda, p. 1508.This article is highlighted in the In This Issue feature, p. 1494.

Published
2018

3. Resource requirements to accelerate clinical applications of next-generation sequencing and radiomics: workshop commentary and review.

Author

Harris, Lyndsay, Shankar, Lalitha K, Hildebrandt, Claire, Rubinstein, Wendy S, Langlais, Kristofor, Rodriguez, Henry, Berger, Adam, Freymann, John, Huang, Erich P, Williams, P Mickey, Zenklusen, Jean Claude, Ochs, Robert, Tezak, Zivana, and Sahiner, Berkman

Subjects
NUCLEOTIDE sequencing, ARTIFICIAL intelligence, MACHINE learning, RADIOMICS, SCIENTIFIC community
Abstract

The National Institutes of Health–US Food and Drug Administration Joint Leadership Council Next-Generation Sequencing and Radiomics Working Group was formed by the National Institutes of Health–Food and Drug Administration Joint Leadership Council to promote the development and validation of innovative next-generation sequencing tests, radiomic tools, and associated data analysis and interpretation enhanced by artificial intelligence and machine learning technologies. A 2-day workshop was held on September 29-30, 2021, to convene members of the scientific community to discuss how to overcome the "ground truth" gap that has frequently been acknowledged as 1 of the limiting factors impeding high-quality research, development, validation, and regulatory science in these fields. This report provides a summary of the resource gaps identified by the working group and attendees, highlights existing resources and the ways they can potentially be employed to accelerate growth in these fields, and presents opportunities to support next-generation sequencing and radiomic tool development and validation using technologies such as artificial intelligence and machine learning. [ABSTRACT FROM AUTHOR]

Published
2024
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4. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

Author

Ding, Li, Bailey, Matthew H, Porta-Pardo, Eduard, Thorsson, Vesteinn, Colaprico, Antonio, Bertrand, Denis, Gibbs, David L, Weerasinghe, Amila, Huang, Kuan-lin, Tokheim, Collin, Cortés-Ciriano, Isidro, Jayasinghe, Reyka, Chen, Feng, Yu, Lihua, Sun, Sam, Olsen, Catharina, Kim, Jaegil, Taylor, Alison M, Cherniack, Andrew D, Akbani, Rehan, Suphavilai, Chayaporn, Nagarajan, Niranjan, Stuart, Joshua M, Mills, Gordon B, Wyczalkowski, Matthew A, Vincent, Benjamin G, Hutter, Carolyn M, Zenklusen, Jean Claude, Hoadley, Katherine A, Wendl, Michael C, Shmulevich, llya, Lazar, Alexander J, Wheeler, David A, Getz, Gad, Network, The Cancer Genome Atlas Research, Caesar-Johnson, Samantha J, Demchok, John A, Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L, Sofia, Heidi J, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C, Zhang, Jiashan, Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Heiman, David I, Lawrence, Michael S, Lin, Pei, Meier, Sam, Noble, Michael S, Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Zhang, Wei, Broom, Bradley M, Hegde, Apurva M, Ju, Zhenlin, Kanchi, Rupa S, Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N, Zhang, Jiexin, and Abeshouse, Adam

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Bioinformatics and Computational Biology, Genetics, Oncology and Carcinogenesis, Cancer, Cancer Genomics, Human Genome, Biotechnology, 2.1 Biological and endogenous factors, Good Health and Well Being, Carcinogenesis, DNA Repair, Databases, Genetic, Genes, Neoplasm, Genomics, Humans, Metabolic Networks and Pathways, Microsatellite Instability, Mutation, Neoplasms, Transcriptome, Tumor Microenvironment, Cancer Genome Atlas Research Network, TCGA, cancer, cancer genomics, omics, oncogenic process, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

The Cancer Genome Atlas (TCGA) has catalyzed systematic characterization of diverse genomic alterations underlying human cancers. At this historic junction marking the completion of genomic characterization of over 11,000 tumors from 33 cancer types, we present our current understanding of the molecular processes governing oncogenesis. We illustrate our insights into cancer through synthesis of the findings of the TCGA PanCancer Atlas project on three facets of oncogenesis: (1) somatic driver mutations, germline pathogenic variants, and their interactions in the tumor; (2) the influence of the tumor genome and epigenome on transcriptome and proteome; and (3) the relationship between tumor and the microenvironment, including implications for drugs targeting driver events and immunotherapies. These results will anchor future characterization of rare and common tumor types, primary and relapsed tumors, and cancers across ancestry groups and will guide the deployment of clinical genomic sequencing.

Published
2018

5. The Integrated Genomic Landscape of Thymic Epithelial Tumors

Author

Radovich, Milan, Pickering, Curtis R, Felau, Ina, Ha, Gavin, Zhang, Hailei, Jo, Heejoon, Hoadley, Katherine A, Anur, Pavana, Zhang, Jiexin, McLellan, Mike, Bowlby, Reanne, Matthew, Thomas, Danilova, Ludmila, Hegde, Apurva M, Kim, Jaegil, Leiserson, Mark DM, Sethi, Geetika, Lu, Charles, Ryan, Michael, Su, Xiaoping, Cherniack, Andrew D, Robertson, Gordon, Akbani, Rehan, Spellman, Paul, Weinstein, John N, Hayes, D Neil, Raphael, Ben, Lichtenberg, Tara, Leraas, Kristen, Zenklusen, Jean Claude, Network, The Cancer Genome Atlas, Ally, Adrian, Appelbaum, Elizabeth L, Auman, J Todd, Balasundaram, Miruna, Balu, Saianand, Behera, Madhusmita, Beroukhim, Rameen, Berrios, Mario, Blandino, Giovanni, Bodenheimer, Tom, Bootwalla, Moiz S, Bowen, Jay, Brooks, Denise, Carcano, Flavio M, Carlsen, Rebecca, Carvalho, Andre L, Castro, Patricia, Chalabreysse, Lara, Chin, Lynda, Cho, Juok, Choe, Gina, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cope, Leslie, Cordes, Matthew G, Crain, Daniel, Curley, Erin, Defreitas, Timothy, Demchok, John A, Detterbeck, Frank, Dhalla, Noreen, Dienemann, Hendrik, Edenfield, W Jeff, Facciolo, Francesco, Ferguson, Martin L, Frazer, Scott, Fronick, Catrina C, Fulton, Lucinda A, Fulton, Robert S, Gabriel, Stacey B, Gardner, Johanna, Gastier-Foster, Julie M, Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Heiman, David I, Hobensack, Shital, Holbrook, Andrea, Holt, Robert A, Hoyle, Alan P, Hutter, Carolyn M, Ittmann, Michael, Jefferys, Stuart R, Jones, Corbin D, Jones, Steven JM, Kasaian, Katayoon, Kimes, Patrick K, Lai, Phillip H, Laird, Peter W, Lawrence, Michael S, Lin, Pei, Liu, Jia, Lolla, Laxmi, Lu, Yiling, Ma, Yussanne, Maglinte, Dennis T, and Mallery, David

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Human Genome, Autoimmune Disease, Cancer, Rare Diseases, Biotechnology, 2.1 Biological and endogenous factors, Inflammatory and immune system, Adolescent, Adult, Aged, Aged, 80 and over, Female, Genomics, Humans, Male, Middle Aged, Mutation, Neoplasms, Glandular and Epithelial, Thymoma, Thymus Neoplasms, Transcription Factors, TFII, Young Adult, Cancer Genome Atlas Network, TCGA, autoimmunity, genomics, myasthenia gravis, proteomics, thymic carcinoma, thymic epithelial tumors, thymoma, transcriptomics, Neurosciences, Oncology and Carcinogenesis, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

Thymic epithelial tumors (TETs) are one of the rarest adult malignancies. Among TETs, thymoma is the most predominant, characterized by a unique association with autoimmune diseases, followed by thymic carcinoma, which is less common but more clinically aggressive. Using multi-platform omics analyses on 117 TETs, we define four subtypes of these tumors defined by genomic hallmarks and an association with survival and World Health Organization histological subtype. We further demonstrate a marked prevalence of a thymoma-specific mutated oncogene, GTF2I, and explore its biological effects on multi-platform analysis. We further observe enrichment of mutations in HRAS, NRAS, and TP53. Last, we identify a molecular link between thymoma and the autoimmune disease myasthenia gravis, characterized by tumoral overexpression of muscle autoantigens, and increased aneuploidy.

Published
2018

6. NCI Cancer Research Data Commons: Resources to Share Key Cancer Data

Author

Wang, Zhining, primary, Davidsen, Tanja M., additional, Kuffel, Gina R., additional, Addepalli, KanakaDurga, additional, Bell, Amanda, additional, Casas-Silva, Esmeralda, additional, Dingerdissen, Hayley, additional, Farahani, Keyvan, additional, Fedorov, Andrey, additional, Gaheen, Sharon, additional, Grossman, Robert L., additional, Kikinis, Ron, additional, Kim, Erika, additional, Otridge, John, additional, Pihl, Todd, additional, Porter, Melissa, additional, Rodriguez, Henry, additional, Staudt, Louis M., additional, Thangudu, Ratna R., additional, Venkatachari, Sudha, additional, Zenklusen, Jean Claude, additional, Zhang, Xu, additional, Barnholtz-Sloan, Jill S., additional, CRDC Program, the, additional, and Kerlavage, Anthony R., additional

Published
2024
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7. Facilitating a culture of responsible and effective sharing of cancer genome data

Author

Siu, Lillian L, Lawler, Mark, Haussler, David, Knoppers, Bartha Maria, Lewin, Jeremy, Vis, Daniel J, Liao, Rachel G, Andre, Fabrice, Banks, Ian, Barrett, J Carl, Caldas, Carlos, Camargo, Anamaria Aranha, Fitzgerald, Rebecca C, Mao, Mao, Mattison, John E, Pao, William, Sellers, William R, Sullivan, Patrick, Teh, Bin Tean, Ward, Robyn L, ZenKlusen, Jean Claude, Sawyers, Charles L, and Voest, Emile E

Subjects
Health Services and Systems, Health Sciences, Health Services, Human Genome, Cancer, Clinical Research, Genetics, Biotechnology, Good Health and Well Being, Computational Biology, Culture, Databases, Genetic, Genome, Humans, Information Dissemination, Neoplasms, Medical and Health Sciences, Immunology, Biomedical and clinical sciences, Health sciences
Abstract

Rapid and affordable tumor molecular profiling has led to an explosion of clinical and genomic data poised to enhance the diagnosis, prognostication and treatment of cancer. A critical point has now been reached at which the analysis and storage of annotated clinical and genomic information in unconnected silos will stall the advancement of precision cancer care. Information systems must be harmonized to overcome the multiple technical and logistical barriers to data sharing. Against this backdrop, the Global Alliance for Genomic Health (GA4GH) was established in 2013 to create a common framework that enables responsible, voluntary and secure sharing of clinical and genomic data. This Perspective from the GA4GH Clinical Working Group Cancer Task Team highlights the data-aggregation challenges faced by the field, suggests potential collaborative solutions and describes how GA4GH can catalyze a harmonized data-sharing culture.

Published
2016

8. 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

10. Table S6 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma

Author

Hmeljak, Julija, primary, Sanchez-Vega, Francisco, primary, Hoadley, Katherine A., primary, Shih, Juliann, primary, Stewart, Chip, primary, Heiman, David, primary, Tarpey, Patrick, primary, Danilova, Ludmila, primary, Drill, Esther, primary, Gibb, Ewan A., primary, Bowlby, Reanne, primary, Kanchi, Rupa, primary, Osmanbeyoglu, Hatice U., primary, Sekido, Yoshitaka, primary, Takeshita, Jumpei, primary, Newton, Yulia, primary, Graim, Kiley, primary, Gupta, Manaswi, primary, Gay, Carl M., primary, Diao, Lixia, primary, Gibbs, David L., primary, Thorsson, Vesteinn, primary, Iype, Lisa, primary, Kantheti, Havish, primary, Severson, David T., primary, Ravegnini, Gloria, primary, Desmeules, Patrice, primary, Jungbluth, Achim A., primary, Travis, William D., primary, Dacic, Sanja, primary, Chirieac, Lucian R., primary, Galateau-Sallé, Françoise, primary, Fujimoto, Junya, primary, Husain, Aliya N., primary, Silveira, Henrique C., primary, Rusch, Valerie W., primary, Rintoul, Robert C., primary, Pass, Harvey, primary, Kindler, Hedy, primary, Zauderer, Marjorie G., primary, Kwiatkowski, David J., primary, Bueno, Raphael, primary, Tsao, Anne S., primary, Creaney, Jenette, primary, Lichtenberg, Tara, primary, Leraas, Kristen, primary, Bowen, Jay, primary, Felau, Ina, primary, Zenklusen, Jean Claude, primary, Akbani, Rehan, primary, Cherniack, Andrew D., primary, Byers, Lauren A., primary, Noble, Michael S., primary, Fletcher, Jonathan A., primary, Robertson, A. Gordon, primary, Shen, Ronglai, primary, Aburatani, Hiroyuki, primary, Robinson, Bruce W., primary, Campbell, Peter, primary, Ladanyi, Marc, primary, Ally, Adrian, primary, Anur, Pavana, primary, Armenia, Joshua, primary, Auman, J. Todd, primary, Balasundaram, Miruna, primary, Balu, Saianand, primary, Baylin, Stephen B., primary, Becich, Michael, primary, Behrens, Carmen, primary, Beroukhim, Rameen, primary, Bielski, Craig, primary, Bodenheimer, Tom, primary, Bootwalla, Moiz S., primary, Brooks, Denise, primary, Byers, Lauren Averett, primary, Cárcano, Flávio M., primary, Carlsen, Rebecca, primary, Carvalho, Andre L., primary, Cheung, Dorothy, primary, Chirieac, Lucian, primary, Cho, Juok, primary, Chuah, Eric, primary, Chudamani, Sudha, primary, Cibulskis, Carrie, primary, Cope, Leslie, primary, Crain, Daniel, primary, Curley, Erin, primary, Rienzo, Assunta De, primary, DeFreitas, Timothy, primary, Demchok, John A., primary, Dhalla, Noreen, primary, Dhir, Rajiv, primary, Feldman, Michael, primary, Ferguson, Martin L., primary, Fukuda, Shiro, primary, Gabriel, Stacey B., primary, Sallé, Françoise Galateau, primary, Gao, Jianjiong, primary, Gardner, Johanna, primary, Gastier-Foster, Julie M., primary, Gehlenborg, Nils, primary, Gerken, Mark, primary, Getz, Gad, primary, Goparaju, Chandra, primary, Gross, Benjamin, primary, Guo, Guangwu, primary, Hasegawa, Seiki, primary, Haussler, David, primary, Hayes, D. Neil, primary, Heiman, David I., primary, Heins, Zachary, primary, Holt, Robert A., primary, Hoyle, Alan P., primary, Husain, Aliya, primary, Hutter, Carolyn M., primary, Jefferys, Stuart R., primary, Jones, Steven J.M., primary, Jones, Corbin D., primary, Kanchi, Rupa S., primary, Kasaian, Katayoon, primary, Kim, Jaegil, primary, Kondo, Nobuyuki, primary, Krausz, Thomas, primary, Kundra, Ritika, primary, Kuribayashi, Kozo, primary, Lai, Phillip H., primary, Laird, Peter W., primary, Lawrence, Michael S., primary, Lee, Darlene, primary, Leraas, Kristen M., primary, Lichtenberg, Tara M., primary, Lin, Pei, primary, Liu, Jia, primary, Liu, Wenbin, primary, Liu, Eric Minwei, primary, Lolla, Laxmi, primary, Longatto-Filho, Adhemar, primary, Lu, Yiling, primary, Luketich, James, primary, Ma, Yussanne, primary, Maglinte, Dennis T., primary, Mallory, David, primary, Marra, Marco A., primary, Mayo, Michael, primary, Meier, Sam, primary, Melamed, Jonathan, primary, Meng, Shaowu, primary, Meyerson, Matthew, primary, Mieczkowski, Piotr A., primary, Mills, Gordon B., primary, Moore, Richard A., primary, Moran, Cesar, primary, Morris, Scott, primary, Mose, Lisle E., primary, Mungall, Andrew J., primary, Mungall, Karen, primary, Nakano, Takashi, primary, Naresh, Rashi, primary, Ochoa, Angelica, primary, Osmanbeyoglu, Hatice, primary, Parker, Joel S., primary, Pass, Harvey I., primary, Paulauskis, Joseph, primary, Pennathur, Arjun, primary, Pennell, Nathan A., primary, Penny, Robert, primary, Perou, Charles M., primary, Pihl, Todd, primary, Ramirez, Nilsa C., primary, Rassl, Doris M., primary, Reid, Glen, primary, Reis, Rui M., primary, Reynolds, Sheila M., primary, Rice, David, primary, Richards, William G, primary, Roach, Jeffrey, primary, Rusch, Valerie, primary, Sadeghi, Sara, primary, Saksena, Gordon, primary, Sander, Chris, primary, Sato, Ayuko, primary, Scapulatempo-Neto, Cristovam, primary, Schein, Jacqueline E., primary, Schultz, Nikolaus, primary, Schumacher, Steven E., primary, Seiwert, Tanguy, primary, Severson, David T, primary, Shelton, Candace, primary, Shelton, Troy, primary, Sheridan, Robert, primary, Shi, Yan, primary, Shiraishi, Yuichi, primary, Shmulevich, Ilya, primary, Silveira, Henrique C. S., primary, Simons, Janae V., primary, Sipahimalani, Payal, primary, Skelly, Tara, primary, Sofia, Heidi J., primary, Soloway, Matthew G., primary, Spellman, Paul, primary, Stuart, Josh, primary, Sun, Qiang, primary, Tam, Angela, primary, Tan, Donghui, primary, Tarnuzzer, Roy, primary, Tatsuno, Kenji, primary, Taylor, Barry S, primary, Thiessen, Nina, primary, Thompson, Eric, primary, Tsao, Anne, primary, Tse, Kane, primary, Tsujimura, Tohru, primary, Valdivieso, Federico, primary, Van Den Berg, David J., primary, van Zandwijk, Nico, primary, Veluvolu, Umadevi, primary, Viana, Luciano S., primary, Voet, Douglas, primary, Wan, Yunhu, primary, Wang, Zhining, primary, Wang, Jing, primary, Weaver, Joellen, primary, Weinstein, John N., primary, Weisenberger, Daniel J., primary, Wilkerson, Matthew D., primary, Wise, Lisa, primary, Wistuba, Ignacio, primary, Wong, Tina, primary, Wu, Ye, primary, Yamamoto, Shogo, primary, Yang, Liming, primary, Zenklusen, Jean C., primary, Zhang, Jiashan, primary, Zhang, Hailei, primary, Zhang, Hongxin, primary, and Zmuda, Erik, primary

Published
2023
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12. Data from Integrative Molecular Characterization of Malignant Pleural Mesothelioma

Author

Hmeljak, Julija, primary, Sanchez-Vega, Francisco, primary, Hoadley, Katherine A., primary, Shih, Juliann, primary, Stewart, Chip, primary, Heiman, David, primary, Tarpey, Patrick, primary, Danilova, Ludmila, primary, Drill, Esther, primary, Gibb, Ewan A., primary, Bowlby, Reanne, primary, Kanchi, Rupa, primary, Osmanbeyoglu, Hatice U., primary, Sekido, Yoshitaka, primary, Takeshita, Jumpei, primary, Newton, Yulia, primary, Graim, Kiley, primary, Gupta, Manaswi, primary, Gay, Carl M., primary, Diao, Lixia, primary, Gibbs, David L., primary, Thorsson, Vesteinn, primary, Iype, Lisa, primary, Kantheti, Havish, primary, Severson, David T., primary, Ravegnini, Gloria, primary, Desmeules, Patrice, primary, Jungbluth, Achim A., primary, Travis, William D., primary, Dacic, Sanja, primary, Chirieac, Lucian R., primary, Galateau-Sallé, Françoise, primary, Fujimoto, Junya, primary, Husain, Aliya N., primary, Silveira, Henrique C., primary, Rusch, Valerie W., primary, Rintoul, Robert C., primary, Pass, Harvey, primary, Kindler, Hedy, primary, Zauderer, Marjorie G., primary, Kwiatkowski, David J., primary, Bueno, Raphael, primary, Tsao, Anne S., primary, Creaney, Jenette, primary, Lichtenberg, Tara, primary, Leraas, Kristen, primary, Bowen, Jay, primary, Felau, Ina, primary, Zenklusen, Jean Claude, primary, Akbani, Rehan, primary, Cherniack, Andrew D., primary, Byers, Lauren A., primary, Noble, Michael S., primary, Fletcher, Jonathan A., primary, Robertson, A. Gordon, primary, Shen, Ronglai, primary, Aburatani, Hiroyuki, primary, Robinson, Bruce W., primary, Campbell, Peter, primary, Ladanyi, Marc, primary, Ally, Adrian, primary, Anur, Pavana, primary, Armenia, Joshua, primary, Auman, J. Todd, primary, Balasundaram, Miruna, primary, Balu, Saianand, primary, Baylin, Stephen B., primary, Becich, Michael, primary, Behrens, Carmen, primary, Beroukhim, Rameen, primary, Bielski, Craig, primary, Bodenheimer, Tom, primary, Bootwalla, Moiz S., primary, Brooks, Denise, primary, Byers, Lauren Averett, primary, Cárcano, Flávio M., primary, Carlsen, Rebecca, primary, Carvalho, Andre L., primary, Cheung, Dorothy, primary, Chirieac, Lucian, primary, Cho, Juok, primary, Chuah, Eric, primary, Chudamani, Sudha, primary, Cibulskis, Carrie, primary, Cope, Leslie, primary, Crain, Daniel, primary, Curley, Erin, primary, Rienzo, Assunta De, primary, DeFreitas, Timothy, primary, Demchok, John A., primary, Dhalla, Noreen, primary, Dhir, Rajiv, primary, Feldman, Michael, primary, Ferguson, Martin L., primary, Fukuda, Shiro, primary, Gabriel, Stacey B., primary, Sallé, Françoise Galateau, primary, Gao, Jianjiong, primary, Gardner, Johanna, primary, Gastier-Foster, Julie M., primary, Gehlenborg, Nils, primary, Gerken, Mark, primary, Getz, Gad, primary, Goparaju, Chandra, primary, Gross, Benjamin, primary, Guo, Guangwu, primary, Hasegawa, Seiki, primary, Haussler, David, primary, Hayes, D. Neil, primary, Heiman, David I., primary, Heins, Zachary, primary, Holt, Robert A., primary, Hoyle, Alan P., primary, Husain, Aliya, primary, Hutter, Carolyn M., primary, Jefferys, Stuart R., primary, Jones, Steven J.M., primary, Jones, Corbin D., primary, Kanchi, Rupa S., primary, Kasaian, Katayoon, primary, Kim, Jaegil, primary, Kondo, Nobuyuki, primary, Krausz, Thomas, primary, Kundra, Ritika, primary, Kuribayashi, Kozo, primary, Lai, Phillip H., primary, Laird, Peter W., primary, Lawrence, Michael S., primary, Lee, Darlene, primary, Leraas, Kristen M., primary, Lichtenberg, Tara M., primary, Lin, Pei, primary, Liu, Jia, primary, Liu, Wenbin, primary, Liu, Eric Minwei, primary, Lolla, Laxmi, primary, Longatto-Filho, Adhemar, primary, Lu, Yiling, primary, Luketich, James, primary, Ma, Yussanne, primary, Maglinte, Dennis T., primary, Mallory, David, primary, Marra, Marco A., primary, Mayo, Michael, primary, Meier, Sam, primary, Melamed, Jonathan, primary, Meng, Shaowu, primary, Meyerson, Matthew, primary, Mieczkowski, Piotr A., primary, Mills, Gordon B., primary, Moore, Richard A., primary, Moran, Cesar, primary, Morris, Scott, primary, Mose, Lisle E., primary, Mungall, Andrew J., primary, Mungall, Karen, primary, Nakano, Takashi, primary, Naresh, Rashi, primary, Ochoa, Angelica, primary, Osmanbeyoglu, Hatice, primary, Parker, Joel S., primary, Pass, Harvey I., primary, Paulauskis, Joseph, primary, Pennathur, Arjun, primary, Pennell, Nathan A., primary, Penny, Robert, primary, Perou, Charles M., primary, Pihl, Todd, primary, Ramirez, Nilsa C., primary, Rassl, Doris M., primary, Reid, Glen, primary, Reis, Rui M., primary, Reynolds, Sheila M., primary, Rice, David, primary, Richards, William G, primary, Roach, Jeffrey, primary, Rusch, Valerie, primary, Sadeghi, Sara, primary, Saksena, Gordon, primary, Sander, Chris, primary, Sato, Ayuko, primary, Scapulatempo-Neto, Cristovam, primary, Schein, Jacqueline E., primary, Schultz, Nikolaus, primary, Schumacher, Steven E., primary, Seiwert, Tanguy, primary, Severson, David T, primary, Shelton, Candace, primary, Shelton, Troy, primary, Sheridan, Robert, primary, Shi, Yan, primary, Shiraishi, Yuichi, primary, Shmulevich, Ilya, primary, Silveira, Henrique C. S., primary, Simons, Janae V., primary, Sipahimalani, Payal, primary, Skelly, Tara, primary, Sofia, Heidi J., primary, Soloway, Matthew G., primary, Spellman, Paul, primary, Stuart, Josh, primary, Sun, Qiang, primary, Tam, Angela, primary, Tan, Donghui, primary, Tarnuzzer, Roy, primary, Tatsuno, Kenji, primary, Taylor, Barry S, primary, Thiessen, Nina, primary, Thompson, Eric, primary, Tsao, Anne, primary, Tse, Kane, primary, Tsujimura, Tohru, primary, Valdivieso, Federico, primary, Van Den Berg, David J., primary, van Zandwijk, Nico, primary, Veluvolu, Umadevi, primary, Viana, Luciano S., primary, Voet, Douglas, primary, Wan, Yunhu, primary, Wang, Zhining, primary, Wang, Jing, primary, Weaver, Joellen, primary, Weinstein, John N., primary, Weisenberger, Daniel J., primary, Wilkerson, Matthew D., primary, Wise, Lisa, primary, Wistuba, Ignacio, primary, Wong, Tina, primary, Wu, Ye, primary, Yamamoto, Shogo, primary, Yang, Liming, primary, Zenklusen, Jean C., primary, Zhang, Jiashan, primary, Zhang, Hailei, primary, Zhang, Hongxin, primary, and Zmuda, Erik, primary

Published
2023
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14. Supplementary Data from Integrative Molecular Characterization of Malignant Pleural Mesothelioma

Author

Hmeljak, Julija, primary, Sanchez-Vega, Francisco, primary, Hoadley, Katherine A., primary, Shih, Juliann, primary, Stewart, Chip, primary, Heiman, David, primary, Tarpey, Patrick, primary, Danilova, Ludmila, primary, Drill, Esther, primary, Gibb, Ewan A., primary, Bowlby, Reanne, primary, Kanchi, Rupa, primary, Osmanbeyoglu, Hatice U., primary, Sekido, Yoshitaka, primary, Takeshita, Jumpei, primary, Newton, Yulia, primary, Graim, Kiley, primary, Gupta, Manaswi, primary, Gay, Carl M., primary, Diao, Lixia, primary, Gibbs, David L., primary, Thorsson, Vesteinn, primary, Iype, Lisa, primary, Kantheti, Havish, primary, Severson, David T., primary, Ravegnini, Gloria, primary, Desmeules, Patrice, primary, Jungbluth, Achim A., primary, Travis, William D., primary, Dacic, Sanja, primary, Chirieac, Lucian R., primary, Galateau-Sallé, Françoise, primary, Fujimoto, Junya, primary, Husain, Aliya N., primary, Silveira, Henrique C., primary, Rusch, Valerie W., primary, Rintoul, Robert C., primary, Pass, Harvey, primary, Kindler, Hedy, primary, Zauderer, Marjorie G., primary, Kwiatkowski, David J., primary, Bueno, Raphael, primary, Tsao, Anne S., primary, Creaney, Jenette, primary, Lichtenberg, Tara, primary, Leraas, Kristen, primary, Bowen, Jay, primary, Felau, Ina, primary, Zenklusen, Jean Claude, primary, Akbani, Rehan, primary, Cherniack, Andrew D., primary, Byers, Lauren A., primary, Noble, Michael S., primary, Fletcher, Jonathan A., primary, Robertson, A. Gordon, primary, Shen, Ronglai, primary, Aburatani, Hiroyuki, primary, Robinson, Bruce W., primary, Campbell, Peter, primary, Ladanyi, Marc, primary, Ally, Adrian, primary, Anur, Pavana, primary, Armenia, Joshua, primary, Auman, J. Todd, primary, Balasundaram, Miruna, primary, Balu, Saianand, primary, Baylin, Stephen B., primary, Becich, Michael, primary, Behrens, Carmen, primary, Beroukhim, Rameen, primary, Bielski, Craig, primary, Bodenheimer, Tom, primary, Bootwalla, Moiz S., primary, Brooks, Denise, primary, Byers, Lauren Averett, primary, Cárcano, Flávio M., primary, Carlsen, Rebecca, primary, Carvalho, Andre L., primary, Cheung, Dorothy, primary, Chirieac, Lucian, primary, Cho, Juok, primary, Chuah, Eric, primary, Chudamani, Sudha, primary, Cibulskis, Carrie, primary, Cope, Leslie, primary, Crain, Daniel, primary, Curley, Erin, primary, Rienzo, Assunta De, primary, DeFreitas, Timothy, primary, Demchok, John A., primary, Dhalla, Noreen, primary, Dhir, Rajiv, primary, Feldman, Michael, primary, Ferguson, Martin L., primary, Fukuda, Shiro, primary, Gabriel, Stacey B., primary, Sallé, Françoise Galateau, primary, Gao, Jianjiong, primary, Gardner, Johanna, primary, Gastier-Foster, Julie M., primary, Gehlenborg, Nils, primary, Gerken, Mark, primary, Getz, Gad, primary, Goparaju, Chandra, primary, Gross, Benjamin, primary, Guo, Guangwu, primary, Hasegawa, Seiki, primary, Haussler, David, primary, Hayes, D. Neil, primary, Heiman, David I., primary, Heins, Zachary, primary, Holt, Robert A., primary, Hoyle, Alan P., primary, Husain, Aliya, primary, Hutter, Carolyn M., primary, Jefferys, Stuart R., primary, Jones, Steven J.M., primary, Jones, Corbin D., primary, Kanchi, Rupa S., primary, Kasaian, Katayoon, primary, Kim, Jaegil, primary, Kondo, Nobuyuki, primary, Krausz, Thomas, primary, Kundra, Ritika, primary, Kuribayashi, Kozo, primary, Lai, Phillip H., primary, Laird, Peter W., primary, Lawrence, Michael S., primary, Lee, Darlene, primary, Leraas, Kristen M., primary, Lichtenberg, Tara M., primary, Lin, Pei, primary, Liu, Jia, primary, Liu, Wenbin, primary, Liu, Eric Minwei, primary, Lolla, Laxmi, primary, Longatto-Filho, Adhemar, primary, Lu, Yiling, primary, Luketich, James, primary, Ma, Yussanne, primary, Maglinte, Dennis T., primary, Mallory, David, primary, Marra, Marco A., primary, Mayo, Michael, primary, Meier, Sam, primary, Melamed, Jonathan, primary, Meng, Shaowu, primary, Meyerson, Matthew, primary, Mieczkowski, Piotr A., primary, Mills, Gordon B., primary, Moore, Richard A., primary, Moran, Cesar, primary, Morris, Scott, primary, Mose, Lisle E., primary, Mungall, Andrew J., primary, Mungall, Karen, primary, Nakano, Takashi, primary, Naresh, Rashi, primary, Ochoa, Angelica, primary, Osmanbeyoglu, Hatice, primary, Parker, Joel S., primary, Pass, Harvey I., primary, Paulauskis, Joseph, primary, Pennathur, Arjun, primary, Pennell, Nathan A., primary, Penny, Robert, primary, Perou, Charles M., primary, Pihl, Todd, primary, Ramirez, Nilsa C., primary, Rassl, Doris M., primary, Reid, Glen, primary, Reis, Rui M., primary, Reynolds, Sheila M., primary, Rice, David, primary, Richards, William G, primary, Roach, Jeffrey, primary, Rusch, Valerie, primary, Sadeghi, Sara, primary, Saksena, Gordon, primary, Sander, Chris, primary, Sato, Ayuko, primary, Scapulatempo-Neto, Cristovam, primary, Schein, Jacqueline E., primary, Schultz, Nikolaus, primary, Schumacher, Steven E., primary, Seiwert, Tanguy, primary, Severson, David T, primary, Shelton, Candace, primary, Shelton, Troy, primary, Sheridan, Robert, primary, Shi, Yan, primary, Shiraishi, Yuichi, primary, Shmulevich, Ilya, primary, Silveira, Henrique C. S., primary, Simons, Janae V., primary, Sipahimalani, Payal, primary, Skelly, Tara, primary, Sofia, Heidi J., primary, Soloway, Matthew G., primary, Spellman, Paul, primary, Stuart, Josh, primary, Sun, Qiang, primary, Tam, Angela, primary, Tan, Donghui, primary, Tarnuzzer, Roy, primary, Tatsuno, Kenji, primary, Taylor, Barry S, primary, Thiessen, Nina, primary, Thompson, Eric, primary, Tsao, Anne, primary, Tse, Kane, primary, Tsujimura, Tohru, primary, Valdivieso, Federico, primary, Van Den Berg, David J., primary, van Zandwijk, Nico, primary, Veluvolu, Umadevi, primary, Viana, Luciano S., primary, Voet, Douglas, primary, Wan, Yunhu, primary, Wang, Zhining, primary, Wang, Jing, primary, Weaver, Joellen, primary, Weinstein, John N., primary, Weisenberger, Daniel J., primary, Wilkerson, Matthew D., primary, Wise, Lisa, primary, Wistuba, Ignacio, primary, Wong, Tina, primary, Wu, Ye, primary, Yamamoto, Shogo, primary, Yang, Liming, primary, Zenklusen, Jean C., primary, Zhang, Jiashan, primary, Zhang, Hailei, primary, Zhang, Hongxin, primary, and Zmuda, Erik, primary

Published
2023
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22. Author Correction: The NCI Genomic Data Commons

Author

Heath, Allison P., Ferretti, Vincent, Agrawal, Stuti, An, Maksim, Angelakos, James C., Arya, Renuka, Bajari, Rosita, Baqar, Bilal, Barnowski, Justin H. B., Burt, Jeffrey, Catton, Ann, Chan, Brandon F., Chu, Fay, Cullion, Kim, Davidsen, Tanja, Do, Phuong-My, Dompierre, Christian, Ferguson, Martin L., Fitzsimons, Michael S., Ford, Michael, Fukuma, Miyuki, Gaheen, Sharon, Ganji, Gajanan L., Garcia, Tzintzuni I., George, Sameera S., Gerhard, Daniela S., Gerthoffert, Francois, Gomez, Fauzi, Han, Kang, Hernandez, Kyle M., Issac, Biju, Jackson, Richard, Jensen, Mark A., Joshi, Sid, Kadam, Ajinkya, Khurana, Aishmit, Kim, Kyle M. J., Kraft, Victoria E., Li, Shenglai, Lichtenberg, Tara M., Lodato, Janice, Lolla, Laxmi, Martinov, Plamen, Mazzone, Jeffrey A., Miller, Daniel P., Miller, Ian, Miller, Joshua S., Miyauchi, Koji, Murphy, Mark W., Nullet, Thomas, Ogwara, Rowland O., Ortuño, Francisco M., Pedrosa, Jesús, Pham, Phuong L., Popov, Maxim Y., Porter, James J., Powell, Raymond, Rademacher, Karl, Reid, Colin P., Rich, Samantha, Rogel, Bessie, Sahni, Himanso, Savage, Jeremiah H., Schmitt, Kyle A., Simmons, Trevar J., Sislow, Joseph, Spring, Jonathan, Stein, Lincoln, Sullivan, Sean, Tang, Yajing, Thiagarajan, Mathangi, Troyer, Heather D., Wang, Chang, Wang, Zhining, West, Bedford L., Wilmer, Alex, Wilson, Shane, Wu, Kaman, Wysocki, William P., Xiang, Linda, Yamada, Joseph T., Yang, Liming, Yu, Christine, Yung, Christina K., Zenklusen, Jean Claude, Zhang, Junjun, Zhang, Zhenyu, Zhao, Yuanheng, Zubair, Ariz, Staudt, Louis M., and Grossman, Robert L.

Published
2021
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23. 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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25. 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

27. Comprehensive genomic characterization of head and neck squamous cell carcinomas

Author

Lawrence, Michael S., Sougnez, Carrie, Lichtenstein, Lee, Cibulskis, Kristian, Lander, Eric, Gabriel, Stacey B., Getz, Gad, Ally, Adrian, Balasundaram, Miruna, Birol, Inanc, Bowlby, Reanne, Brooks, Denise, Butterfield, Yaron S. N., Carlsen, Rebecca, Cheng, Dean, Chu, Andy, Dhalla, Noreen, Guin, Ranabir, Holt, Robert A., Jones, Steven J. M., Lee, Darlene, Li, Haiyan I., Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Robertson, Gordon A., Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Wong, Tina, Protopopov, Alexei, Santoso, Netty, Lee, Semin, Parfenov, Michael, Zhang, Jianhua, Mahadeshwar, Harshad S., Tang, Jiabin, Ren, Xiaojia, Seth, Sahil, Haseley, Psalm, Zeng, Dong, Yang, Lixing, Xu, Andrew W., Song, Xingzhi, Pantazi, Angeliki, Bristow, Christopher A., Hadjipanayis, Angela, Seidman, Jonathan, Chin, Lynda, Park, Peter J., Kucherlapati, Raju, Akbani, Rehan, Casasent, Tod, Liu, Wenbin, Lu, Yiling, Mills, Gordon, Motter, Thomas, Weinstein, John, Diao, Lixia, Wang, Jing, Fan, You Hong, Liu, Jinze, Wang, Kai, Auman, Todd J., Balu, Saianand, Bodenheimer, Thomas, Buda, Elizabeth, Hayes, Neil D., Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Kimes, Patrick K., Liu, Yufeng, Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Parker, Joel S., Perou, Charles M., Prins, Jan F., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Singh, Darshan, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Walter, Vonn, Waring, Scot, Wilkerson, Matthew D., Wu, Junyuan, Zhao, Ni, Cherniack, Andrew D., Hammerman, Peter S., Tward, Aaron D., Pedamallu, Chandra Sekhar, Saksena, Gordon, Jung, Joonil, Ojesina, Akinyemi I., Carter, Scott L., Zack, Travis I., Schumacher, Steven E., Beroukhim, Rameen, Freeman, Samuel S., Meyerson, Matthew, Cho, Juok, Noble, Michael S., DiCara, Daniel, Zhang, Hailei, Heiman, David I., Gehlenborg, Nils, Voet, Doug, Lin, Pei, Frazer, Scott, Stojanov, Petar, Liu, Yingchun, Zou, Lihua, Kim, Jaegil, Muzny, Donna, Doddapaneni, HarshaVardhan, Kovar, Christie, Reid, Jeff, Morton, Donna, Han, Yi, Hale, Walker, Chao, Hsu, Chang, Kyle, Drummond, Jennifer A., Gibbs, Richard A., Kakkar, Nipun, Wheeler, David, Xi, Liu, Ciriello, Giovanni, Ladanyi, Marc, Lee, William, Ramirez, Ricardo, Sander, Chris, Shen, Ronglai, Sinha, Rileen, Weinhold, Nils, Taylor, Barry S., Aksoy, Arman B., Dresdner, Gideon, Gao, Jianjiong, Gross, Benjamin, Jacobsen, Anders, Reva, Boris, Schultz, Nikolaus, Sumer, Onur S., Sun, Yichao, Chan, Timothy A., Morris, Luc G., Stuart, Joshua, Benz, Stephen, Ng, Sam, Benz, Christopher, Yau, Christina, Baylin, Stephen B., Cope, Leslie, Danilova, Ludmila, Herman, James G., Bootwalla, Moiz, Maglinte, Dennis T., Laird, Peter W., Triche, Timothy, Jr, Weisenberger, Daniel J., Van Den Berg, David J., Agrawal, Nishant, Bishop, Justin, Boutros, Paul C., Bruce, Jeff P., Byers, Lauren Averett, Califano, Joseph, Carey, Thomas E., Chen, Zhong, Cheng, Hui, Chiosea, Simion I., Cohen, Ezra, Diergaarde, Brenda, Egloff, Ann Marie, El-Naggar, Adel K., Ferris, Robert L., Frederick, Mitchell J., Grandis, Jennifer R., Guo, Yan, Haddad, Robert I., Harris, Thomas, Hui, Angela B. Y., Lee, Jack J., Lippman, Scott M., Liu, Fei-Fei, McHugh, Jonathan B., Myers, Jeff, Ng, Patrick Kwok Shing, Perez-Ordonez, Bayardo, Pickering, Curtis R., Prystowsky, Michael, Romkes, Marjorie, Saleh, Anthony D., Sartor, Maureen A., Seethala, Raja, Seiwert, Tanguy Y., Si, Han, Van Waes, Carter, Waggott, Daryl M., Wiznerowicz, Maciej, Yarbrough, Wendell G., Zhang, Jiexin, Zuo, Zhixiang, Burnett, Ken, Crain, Daniel, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Sherman, Mark, Yena, Peggy, Black, Aaron D., Bowen, Jay, Frick, Jessica, Gastier-Foster, Julie M., Harper, Hollie A., Leraas, Kristen, Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Baboud, Julien, Jensen, Mark A., Kahn, Ari B., Pihl, Todd D., Pot, David A., Srinivasan, Deepak, Walton, Jessica S., Wan, Yunhu, Burton, Robert A., Davidsen, Tanja, Demchok, John A., Eley, Greg, Ferguson, Martin L., Shaw, Kenna Mills R., Ozenberger, Bradley A., Sheth, Margi, Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean Claude, Saller, Charles, Tarvin, Katherine, Chen, Chu, Bollag, Roni, Weinberger, Paul, Golusiński, Wojciech, Golusiński, Paweł, Ibbs, Matthew, Korski, Konstanty, Mackiewicz, Andrzej, Suchorska, Wiktoria, Szybiak, Bartosz, Curley, Erin, Beard, Christina, Mitchell, Colleen, Sandusky, George, Ahn, Julie, Khan, Zubair, Irish, Jonathan, Waldron, John, William, William N., Jr, Egea, Sophie, Gomez-Fernandez, Carmen, Herbert, Lynn, Bradford, Carol R., Chepeha, Douglas B., Haddad, Andrea S., Jones, Tamara R., Komarck, Christine M., Malakh, Mayya, Moyer, Jeffrey S., Nguyen, Ariane, Peterson, Lisa A., Prince, Mark E., Rozek, Laura S., Taylor, Evan G., Walline, Heather M., Wolf, Gregory T., Boice, Lori, Chera, Bhishamjit S., Funkhouser, William K., Gulley, Margaret L., Hackman, Trevor G., Hayward, Michele C., Huang, Mei, Rathmell, Kimryn W., Salazar, Ashley H., Shockley, William W., Shores, Carol G., Thorne, Leigh, Weissler, Mark C., Wrenn, Sylvia, Zanation, Adam M., Brown, Brandee T., and Pham, Michelle

Published
2015
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29. Epigenetic-Mediated Dysfunction of the Bone Morphogenetic Protein Pathway Inhibits Differentiation of Glioblastoma-Initiating Cells

Author

Lee, Jeongwu, Son, Myung Jin, Woolard, Kevin, Donin, Nicholas M., Li, Aiguo, Cheng, Chui H., Kotliarova, Svetlana, Kotliarov, Yuri, Walling, Jennifer, Ahn, Susie, Kim, Misuk, Totonchy, Mariam, Cusack, Thomas, Ene, Chibawanye, Ma, Hilary, Su, Qin, Zenklusen, Jean Claude, Zhang, Wei, Maric, Dragan, and Fine, Howard A.

Published
2008
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30. 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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31. Comprehensive molecular characterization of urothelial bladder carcinoma

Author

Weinstein, John N., Akbani, Rehan, Broom, Bradley M., Wang, Wenyi, Verhaak, Roeland G. W., McConkey, David, Lerner, Seth, Morgan, Margaret, Creighton, Chad J., Smith, Carolyn, Kwiatkowski, David J., Cherniack, Andrew D., Kim, Jaegil, Pedamallu, Chandra Sekhar, Noble, Michael S., Al-Ahmadie, Hikmat A., Reuter, Victor E., Rosenberg, Jonathan E., Bajorin, Dean F., Bochner, Bernard H., Solit, David B., Koppie, Theresa, Robinson, Brian, Gordenin, Dmitry A., Fargo, David, Klimczak, Leszek J., Roberts, Steven A., Au, Jessie, Laird, Peter W., Hinoue, Toshinori, Schultz, Nikolaus, Ramirez, Ricardo, Hansel, Donna, Hoadley, Katherine A., Kim, William Y., Damrauer, Jeffrey S., Baylin, Stephen B., Mungall, Andrew J., Robertson, Gordon A., Chu., Andy, Sougnez, Carrie, Cibulskis, Kristian, Lichtenstein, Lee, Sivachenko, Andrey, Stewart, Chip, Lawrence, Michael S., Getz, Gad, Lander, Eric, Gabriel., Stacey B., Donehower, Lawrence, Carter, Scott L., Saksena, Gordon, Schumacher, Steven E., Freeman, Samuel S., Jung, Joonil, Bhatt, Ami S., Pugh, Trevor, Beroukhim, Rameen, Gabriel, Stacey B., Meyerson, Matthew, Chu, Andy, Ally, Adrian, Balasundaram, Miruna, Butterfield, Yaron S. N., Dhalla, Noreen, Hirst, Carrie, Holt, Robert A., Jones, Steven J. M., Lee, Darlene, Li, Haiyan I., Marra, Marco A., Mayo, Michael, Moore, Richard A., Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Wong, Tina, Wye, Natasja, Bowlby, Reanne, Chuah, Eric, Guin, Ranabir, Shen, Hui, Bootwalla, Moiz S., Jr, Timothy Triche, Lai, Phillip H., Van Den Berg, David J., Weisenberger, Daniel J., Balu, Saianand, Bodenheimer, Tom, Damrauer Alan P. Hoyle, Jeffrey S., Jefferys, Stuart R., Meng, Shaowu, Mose, Lisle E., Simons, Janae V., Soloway, Mathew G., Wu, Junyuan, Parker, Joel S., Hayes, Neil D., Roach, Jeffrey, Buda, Elizabeth, Jones, Corbin D., Mieczkowski, Piotr A., Tan, Donghui, Veluvolu, Umadevi, Waring, Scot, Auman, Todd J., Perou, Charles M., Wilkerson, Matthew D., Santoso, Netty, Parfenov, Michael, Ren, Xiaojia, Pantazi, Angeliki, Hadjipanayis, Angela, Seidman, Jonathan, Kucherlapati, Raju, Lee, Semin, Yang, Lixing, Park, Peter J., Xu, Andrew Wei, Protopopov, Alexei, Zhang, Jianhua, Bristow, Christopher, Mahadeshwar, Harshad S., Seth, Sahil, Song, Xingzhi, Tang, Jiabin, Zeng, Dong, Chin, Lynda, Guo, Charles, Casasent, Tod D., Liu, Wenbin, Ju, Zhenlin, Motter, Thomas, Peng, Bo, Ryan, Michael, Su, Xiaoping, Yang, Ji-Yeon, Lorenzi, Philip L., Yao, Hui, Zhang, Nianxiang, Zhang, Jiexin, Mills, Gordon B., Cho, Juok, DiCara, Daniel, Frazer, Scott, Gehlenborg, Nils, Heiman, David I., Lin, Pei, Liu, Yingchun, Stojanov, Petar, Voet, Doug, Zhang, Hailei, Zou, Lihua, Bernard, Brady, Kreisberg, Dick, Reynolds, Sheila, Rovira, Hector, Shmulevich, Ilya, Gao, Jianjiong, Jacobsen, Anders, Aksoy, Arman B., Antipin, Yevgeniy, Ciriello, Giovanni, Dresdner, Gideon, Gross, Benjamin, Lee, William, Reva, Boris, Shen, Ronglai, Sinha, Rileen, Sumer, Onur S., Weinhold, Nils, Ladanyi, Marc, Sander, Chris, Benz, Christopher, Carlin, Daniel, Haussler, David, Ng, Sam, Paull, Evan O., Stuart, Joshua, Zhu, Jing, Liu, Yuexin, Zhang, Wei, Taylor, Barry S., Lichtenberg, Tara M., Zmuda, Erik, Barr, Thomas, Black, Aaron D., George, Myra, Hanf, Benjamin, Helsel, Carmen, McAllister, Cynthia, Ramirez, Nilsa C., Tabler, Teresa R., Weaver, Stephanie, Wise, Lisa, Bowen, Jay, Gastier-Foster, Julie M., Jian, Weiguo, Tello, Sebrina, Ittman, Michael, Castro, Patricia, McClenden, Whitney D., Gibbs, Richard, Saller, Charles, Tarvin, Katherine, DiPiero, Jennifer M., Owens, Jennifer, Bollag, Roni, Li, Qiang, Weinberger, Paul, Czerwinski, Christine, Huelsenbeck-Dill, Lori, Iacocca, Mary, Petrelli, Nicholas, Rabeno, Brenda, Swanson, Pat, Shelton, Troy, Curley, Erin, Gardner, Johanna, Mallery, David, Penny, Robert, Van Bang, Nguyen, Thi Hanh, Phan, Kohl, Bernard, Van Le, Xuan, Duc Phu, Bui, Thorp, Richard, Tien, Nguyen Viet, Vinh, Le Quang, Sandusky, George, Burks, Eric, Christ, Kimberly, Gee, Jason, Holway, Antonia, Moinzadeh, Alireza, Sorcini, Andrea, Sullivan, Travis, Garcia-Grossman, Ilana R., Regazzi, Ashley M., Boice, Lori, Rathmell, Wendy Kimryn, Thorne, Leigh, Bastacky, Sheldon, Davies, Benjamin, Dhir, Rajiv, Gingrich, Jeffrey, Hrebinko, Ronald, Maranchie, Jodi, Nelson, Joel, Parwani, Anil, Bshara, Wiam, Gaudioso, Carmelo, Morrison, Carl, Alexopoulou, Vina, Bartlett, John, Engel, Jay, Kodeeswaran, Sugy, Antic, Tatjana, O’Donnell, Peter H., Smith, Norm D., Steinberg, Gary D., Egea, Sophie, Gomez-Fernandez, Carmen, Herbert, Lynn, Jorda, Merce, Soloway, Mark, Beaver, Allison, Carter, Suzie, Kapur, Payal, Lewis, Cheryl, Lotan, Yair, Bondaruk, Jolanta, Czerniak, Bogdan, Skinner, Eila, Aldape, Kenneth, Jensen, Mark A., Kahn, Ari B., Pihl, Todd D., Pot, David A., Srinivasan, Deepak, Wan, Yunhu, Ferguson, Martin L., Zenklusen, Jean Claude, Davidsen, Tanja, Demchok, John A., Mills Shaw, Kenna R., Sheth, Margi, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Hutter, Carolyn, Ozenberger, Bradley A., Sofia, Heidi J., and Eley, Greg

Published
2014
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33. The NCI Genomic Data Commons

Author

Heath, Allison P., primary, Ferretti, Vincent, additional, Agrawal, Stuti, additional, An, Maksim, additional, Angelakos, James C., additional, Arya, Renuka, additional, Bajari, Rosita, additional, Baqar, Bilal, additional, Barnowski, Justin H. B., additional, Burt, Jeffrey, additional, Catton, Ann, additional, Chan, Brandon F., additional, Chu, Fay, additional, Cullion, Kim, additional, Davidsen, Tanja, additional, Do, Phuong-My, additional, Dompierre, Christian, additional, Ferguson, Martin L., additional, Fitzsimons, Michael S., additional, Ford, Michael, additional, Fukuma, Miyuki, additional, Gaheen, Sharon, additional, Ganji, Gajanan L., additional, Garcia, Tzintzuni I., additional, George, Sameera S., additional, Gerhard, Daniela S., additional, Gerthoffert, Francois, additional, Gomez, Fauzi, additional, Han, Kang, additional, Hernandez, Kyle M., additional, Issac, Biju, additional, Jackson, Richard, additional, Jensen, Mark A., additional, Joshi, Sid, additional, Kadam, Ajinkya, additional, Khurana, Aishmit, additional, Kim, Kyle M. J., additional, Kraft, Victoria E., additional, Li, Shenglai, additional, Lichtenberg, Tara M., additional, Lodato, Janice, additional, Lolla, Laxmi, additional, Martinov, Plamen, additional, Mazzone, Jeffrey A., additional, Miller, Daniel P., additional, Miller, Ian, additional, Miller, Joshua S., additional, Miyauchi, Koji, additional, Murphy, Mark W., additional, Nullet, Thomas, additional, Ogwara, Rowland O., additional, Ortuño, Francisco M., additional, Pedrosa, Jesús, additional, Pham, Phuong L., additional, Popov, Maxim Y., additional, Porter, James J., additional, Powell, Raymond, additional, Rademacher, Karl, additional, Reid, Colin P., additional, Rich, Samantha, additional, Rogel, Bessie, additional, Sahni, Himanso, additional, Savage, Jeremiah H., additional, Schmitt, Kyle A., additional, Simmons, Trevar J., additional, Sislow, Joseph, additional, Spring, Jonathan, additional, Stein, Lincoln, additional, Sullivan, Sean, additional, Tang, Yajing, additional, Thiagarajan, Mathangi, additional, Troyer, Heather D., additional, Wang, Chang, additional, Wang, Zhining, additional, West, Bedford L., additional, Wilmer, Alex, additional, Wilson, Shane, additional, Wu, Kaman, additional, Wysocki, William P., additional, Xiang, Linda, additional, Yamada, Joseph T., additional, Yang, Liming, additional, Yu, Christine, additional, Yung, Christina K., additional, Zenklusen, Jean Claude, additional, Zhang, Junjun, additional, Zhang, Zhenyu, additional, Zhao, Yuanheng, additional, Zubair, Ariz, additional, Staudt, Louis M., additional, and Grossman, Robert L., additional

Published
2021
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34. Molecular Features of Cancers Exhibiting Exceptional Responses to Treatment

Author

Wheeler, David A., primary, Takebe, Naoko, additional, Hinoue, Toshinori, additional, Hoadley, Katherine A., additional, Cardenas, Maria F., additional, Hamilton, Alina M., additional, Laird, Peter W., additional, Wang, Linghua, additional, Johnson, Adrienne, additional, Dewal, Ninad, additional, Miller, Vincent, additional, Piñeyro, David, additional, Castro de Moura, Manuel, additional, Esteller, Manel, additional, Shen, Hui, additional, Zenklusen, Jean Claude, additional, Tarnuzzer, Roy, additional, McShane, Lisa M., additional, Tricoli, James V., additional, Williams, Paul M., additional, Lubensky, Irina, additional, O'Sullivan-Coyne, Geraldine, additional, Kohn, Elise C., additional, Little, Richard F., additional, White, Jeffrey, additional, Malik, Shakun, additional, Harris, Lyndsay, additional, Weil, Carol, additional, Chen, Alice P., additional, Karlovich, Chris, additional, Rodgers, Brian, additional, Shankar, Lalitha, additional, Jacobs, Paula, additional, Nolan, Tracy, additional, Hu, Jianhong, additional, Muzny, Donna M., additional, Doddapaneni, Harshavardhan, additional, Korchina, Viktoriya, additional, Gastier-Foster, Julie, additional, Bowen, Jay, additional, Leraas, Kristen, additional, Edmondson, Elijah F., additional, Doroshow, James H., additional, Conley, Barbara A., additional, Ivy, S. Percy, additional, and Staudt, Louis M., additional

Published
2021
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36. The Exceptional Responders Initiative: Feasibility of a National Cancer Institute Pilot Study

Author

Conley, Barbara A, primary, Staudt, Lou, additional, Takebe, Naoko, additional, Wheeler, David A, additional, Wang, Linghua, additional, Cardenas, Maria F, additional, Korchina, Viktoriya, additional, Zenklusen, Jean Claude, additional, McShane, Lisa M, additional, Tricoli, James V, additional, Williams, Paul M, additional, Lubensky, Irina, additional, O’Sullivan-Coyne, Geraldine, additional, Kohn, Elise, additional, Little, Richard F, additional, White, Jeffrey, additional, Malik, Shakun, additional, Harris, Lyndsay N, additional, Mann, Bhupinder, additional, Weil, Carol, additional, Tarnuzzer, Roy, additional, Karlovich, Chris, additional, Rodgers, Brian, additional, Shankar, Lalitha, additional, Jacobs, Paula M, additional, Nolan, Tracy, additional, Berryman, Sean M, additional, Gastier-Foster, Julie, additional, Bowen, Jay, additional, Leraas, Kristen, additional, Shen, Hui, additional, Laird, Peter W, additional, Esteller, Manel, additional, Miller, Vincent, additional, Johnson, Adrienne, additional, Edmondson, Elijah F, additional, Giordano, Thomas J, additional, Kim, Benjamin, additional, and Ivy, S Percy, additional

Published
2020
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38. CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations

Author

Zenklusen Jean-Claude, Wuchty Stefan, Cheng Hangjiong, Bozdag Serdar, Kotliarov Yuri, and Fine Howard A

Subjects
Internal medicine, RC31-1245, Genetics, QH426-470
Abstract

Abstract Background Genomic copy number alterations are widely associated with a broad range of human tumors and offer the potential to be used as a diagnostic tool. Especially in the emerging era of personalized medicine medical informatics tools that allow the fast visualization and analysis of genomic alterations of a patient's genomic profile for diagnostic and potential treatment purposes increasingly gain importance. Results We developed CNAReporter, a software tool that allows users to visualize SNP-specific data obtained from Affymetrix arrays and generate PDF-reports as output. We combined standard algorithms for the analysis of chromosomal alterations, utilizing the widely applied GenePattern framework. As an example, we show genome analyses of two patients with distinctly different CNA profiles using the tool. Conclusions Glioma subtypes, characterized by different genomic alterations, are often treated differently but can be difficult to differentiate pathologically. CNAReporter offers a user-friendly way to visualize and analyse genomic changes of any given tumor genomic profile, thereby leading to an accurate diagnosis and patient-specific treatment.

Published
2010
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39. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

Author

Onderzoeksgroep 6, Pathologie Pathologen staf, Ding, Li, Bailey, Matthew H., Porta-Pardo, Eduard, Thorsson, Vesteinn, Colaprico, Antonio, Bertrand, Denis, Gibbs, David L., Weerasinghe, Amila, Huang, Kuan lin, Tokheim, Collin, Cortés-Ciriano, Isidro, Jayasinghe, Reyka, Chen, Feng, Yu, Lihua, Sun, Sam, Olsen, Catharina, Kim, Jaegil, Taylor, Alison M., Cherniack, Andrew D., Akbani, Rehan, Suphavilai, Chayaporn, Nagarajan, Niranjan, Stuart, Joshua M., Mills, Gordon B., Wyczalkowski, Matthew A., Vincent, Benjamin G., Hutter, Carolyn M., Zenklusen, Jean Claude, Hoadley, Katherine A., Wendl, Michael C., Shmulevich, llya, Lazar, Alexander J., Wheeler, David A., Getz, Gad, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, de Krijger, Ronald, The Cancer Genome Atlas Research Network, Onderzoeksgroep 6, Pathologie Pathologen staf, Ding, Li, Bailey, Matthew H., Porta-Pardo, Eduard, Thorsson, Vesteinn, Colaprico, Antonio, Bertrand, Denis, Gibbs, David L., Weerasinghe, Amila, Huang, Kuan lin, Tokheim, Collin, Cortés-Ciriano, Isidro, Jayasinghe, Reyka, Chen, Feng, Yu, Lihua, Sun, Sam, Olsen, Catharina, Kim, Jaegil, Taylor, Alison M., Cherniack, Andrew D., Akbani, Rehan, Suphavilai, Chayaporn, Nagarajan, Niranjan, Stuart, Joshua M., Mills, Gordon B., Wyczalkowski, Matthew A., Vincent, Benjamin G., Hutter, Carolyn M., Zenklusen, Jean Claude, Hoadley, Katherine A., Wendl, Michael C., Shmulevich, llya, Lazar, Alexander J., Wheeler, David A., Getz, Gad, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, de Krijger, Ronald, and The Cancer Genome Atlas Research Network

Published
2018

40. The International Collaboration for Cancer Classification and Research.

Author

Cree, Ian A., Indave Ruiz, Blanca Iciar, Zavadil, Jiri, McKay, James, Olivier, Magali, Kozlakidis, Zisis, Lazar, Alexander J., Hyde, Chris, Holdenrieder, Stefan, Hastings, Ros, Rajpoot, Nasir, Fouchardiere, Arnaud, Rous, Brian, Zenklusen, Jean Claude, Normanno, Nicola, and Schilsky, Richard L.

Subjects
TUMOR classification, CANCER research, INFORMATION overload, CLASSIFICATION, TRANSLATIONAL research
Abstract

Gaps in the translation of research findings to clinical management have been recognized for decades. They exist for the diagnosis as well as the management of cancer. The international standards for cancer diagnosis are contained within the World Health Organization (WHO) Classification of Tumours, published by the International Agency for Research on Cancer (IARC) and known worldwide as the WHO Blue Books. In addition to their relevance to individual patients, these volumes provide a valuable contribution to cancer research and surveillance, fulfilling an important role in scientific evidence synthesis and international standard setting. However, the multidimensional nature of cancer classification, the way in which the WHO Classification of Tumours is constructed, and the scientific information overload in the field pose important challenges for the translation of research findings to tumour classification and hence cancer diagnosis. To help address these challenges, we have established the International Collaboration for Cancer Classification and Research (IC3R) to provide a forum for the coordination of efforts in evidence generation, standard setting and best practice recommendations in the field of tumour classification. The first IC3R meeting, held in Lyon, France, in February 2019, gathered representatives of major institutions involved in tumour classification and related fields to identify and discuss translational challenges in data comparability, standard setting, quality management, evidence evaluation and copyright, as well as to develop a collaborative plan for addressing these challenges. What's new? The World Health Organization Classification of Tumours has been informing cancer research and clinical practice by providing an international consensus on the tumour criteria for cancer diagnosis. In a new initiative coordinated by the International Agency for Research on Cancer, major institutions are now joining forces to address the remaining challenges in translational research and facilitate the application of research results to clinical practice. The newly‐established International Collaboration for Cancer Classification and Research (IC3R) aims to provide a forum for the coordination of efforts in generating evidence, setting standards, and providing best practice recommendations for tumor classification and cancer research. [ABSTRACT FROM AUTHOR]

Published
2021
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41. The Exceptional Responders Initiative: Feasibility of a National Cancer Institute Pilot Study.

Author

Conley, Barbara A, Staudt, Lou, Takebe, Naoko, Wheeler, David A, Wang, Linghua, Cardenas, Maria F, Korchina, Viktoriya, Zenklusen, Jean Claude, McShane, Lisa M, Tricoli, James V, Williams, Paul M, Lubensky, Irina, O'Sullivan-Coyne, Geraldine, Kohn, Elise, Little, Richard F, White, Jeffrey, Malik, Shakun, Harris, Lyndsay N, Mann, Bhupinder, and Weil, Carol

Subjects
INVESTIGATIONAL therapies, PILOT projects, NUCLEOTIDE sequence, TUMOR treatment, NUCLEIC acids, SEQUENCE analysis, GENETIC mutation, RETROSPECTIVE studies, GENE expression profiling, RESEARCH funding, TUMORS
Abstract

Background: Tumor molecular profiling from patients experiencing exceptional responses to systemic therapy may provide insights into cancer biology and improve treatment tailoring. This pilot study evaluates the feasibility of identifying exceptional responders retrospectively, obtaining pre-exceptional response treatment tumor tissues, and analyzing them with state-of-the-art molecular analysis tools to identify potential molecular explanations for responses.Methods: Exceptional response was defined as partial (PR) or complete (CR) response to a systemic treatment with population PR or CR rate less than 10% or an unusually long response (eg, duration >3 times published median). Cases proposed by patients' clinicians were reviewed by clinical and translational experts. Tumor and normal tissue (if possible) were profiled with whole exome sequencing and, if possible, targeted deep sequencing, RNA sequencing, methylation arrays, and immunohistochemistry. Potential germline mutations were tracked for relevance to disease.Results: Cases reflected a variety of tumors and standard and investigational treatments. Of 520 cases, 476 (91.5%) were accepted for further review, and 222 of 476 (46.6%) proposed cases met requirements as exceptional responders. Clinical data were obtained from 168 of 222 cases (75.7%). Tumor was provided from 130 of 168 cases (77.4%). Of 117 of the 130 (90.0%) cases with sufficient nucleic acids, 109 (93.2%) were successfully analyzed; 6 patients had potentially actionable germline mutations.Conclusion: Exceptional responses occur with standard and investigational treatment. Retrospective identification of exceptional responders, accessioning, and sequencing of pretreatment archived tissue is feasible. Data from molecular analyses of tumors, particularly when combining results from patients who received similar treatments, may elucidate molecular bases for exceptional responses. [ABSTRACT FROM AUTHOR]

Published
2021
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44. Distinct Epigenetic Shift in a Subset of Glioma CpG Island Methylator Phenotype (G-CIMP) During Tumor Recurrence

Author

Ferreira de Souza, Camila, primary, Sabedot, Thais S., additional, Malta, Tathiane M., additional, Stetson, Lindsay, additional, Morozova, Olena, additional, Sokolov, Artem, additional, Laird, Peter, additional, Wiznerowicz, Maciej, additional, Iavarone, Antonio, additional, Snyder, James, additional, deCarvalho, Ana, additional, Sanborn, Zachary, additional, McDonald, Kerrie, additional, Friedman, William A., additional, Tirapelli, Daniela, additional, Poisson, Laila, additional, Mikkelsen, Tom, additional, Carlotti, Carlos G., additional, Kalkanis, Steven, additional, Zenklusen, Jean Claude, additional, Salama, Sofie R., additional, Barnholtz-Sloan, Jill, additional, and Noushmehr, Houtan, additional

Published
2018
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45. Core Clinical Data Elements for Cancer Genomic Repositories: A Multi-stakeholder Consensus

Author

Conley, Robert B., primary, Dickson, Dane, additional, Zenklusen, Jean Claude, additional, Al Naber, Jennifer, additional, Messner, Donna A., additional, Atasoy, Ajlan, additional, Chaihorsky, Lena, additional, Collyar, Deborah, additional, Compton, Carolyn, additional, Ferguson, Martin, additional, Khozin, Sean, additional, Klein, Roger D., additional, Kotte, Sri, additional, Kurzrock, Razelle, additional, Lin, C. Jimmy, additional, Liu, Frank, additional, Marino, Ingrid, additional, McDonough, Robert, additional, McNeal, Amy, additional, Miller, Vincent, additional, Schilsky, Richard L., additional, and Wang, Lisa I., additional

Published
2017
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46. AB007. OS02.01. The integrated genomic landscape of thymic epithelial tumors: a report by the TCGA research network

Author

Radovich, Milan, primary, Pickering, Curtis, additional, Felau, Ina, additional, Ha, Gavin, additional, Zhang, Hailei, additional, Jo, Heejoon, additional, Hoadley, Katherine A., additional, Anur, Pavana, additional, Zhang, Jiexin, additional, Mclellan, Mike, additional, Bowlby, Reanne, additional, Matthew, Thomas, additional, Danilova, Ludmila, additional, Hedge, Apurva M., additional, Kim, Jaegil, additional, Leiserson, Max, additional, Sethi, Geetika, additional, Lu, Charles, additional, Ryan, Michael, additional, Su, Xiaoping, additional, Cherniack, Andrew D., additional, Robertson, Gordon, additional, Akbani, Rehan, additional, Spellman, Paul, additional, Weinstein, John N., additional, Hayes, David Neil, additional, Raphael, Ben, additional, Lichtenberg, Tara, additional, Leraas, Kristen, additional, Zenklusen, Jean Claude, additional, Fujimoto, Junya, additional, Scapulatempo-Neto, Cristovam, additional, Moreira, Andre L., additional, Hwang, David, additional, Huang, James, additional, Marino, Mirella, additional, Korst, Robert, additional, Giaccone, Giuseppe, additional, Gokmen-Polar, Yesim, additional, Badve, Sunil, additional, Rajan, Arun, additional, Ströbel, Philipp, additional, Girard, Nicolas, additional, Tsao, Ming S., additional, Marx, Alexander, additional, Tsao, Anne S., additional, and Loehrer, Patrick J., additional

Published
2017
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47. 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

48. Abstract 5287: Heterogeneity of mutation calling and annotation: a survey of cancer next-generation sequencing initiatives by the Global Alliance for Genomics and Health (GA4GH)

Author

Vis, Daniel J., primary, Lewin, Jeremy, additional, Siu, Lillian, additional, Liao, Rachel, additional, Zenklusen, Jean Claude, additional, Calvo, Fabien, additional, Szepessy, Edit, additional, Vivancos, Ana, additional, Wirta, Valtteri, additional, Madhavan, Subha, additional, Park, Keunchil, additional, Tan, Daniel, additional, Laskin, Janessa, additional, Brammer, Melissa, additional, Dias-Neto, Emmanuel, additional, Tolcher, Anthony, additional, Hudson, Thomas J., additional, Sawyers, Charles, additional, Lawler, Mark, additional, and Voest, Emile E., additional

Published
2016
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49. Abstract 612: The NCI exceptional responders initiatives: Initial feasibility result

Author

Conley, Barbara A., primary, Ivy, S Percy, additional, Tricoli, James V., additional, Zenklusen, Jean-Claude, additional, Tarnuzzer, Roy, additional, Lubensky, Irina, additional, Takebe, Naoko, additional, Williams, Paul M., additional, Zujewski, JoAnne, additional, Little, Richard, additional, White, Jeffrey, additional, Kohn, Elise, additional, Malik, Shakun, additional, Kim, Ben, additional, Souhan, Erin, additional, and Staudt, Lou, additional

Published
2015
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50. Comprehensive molecular profiling of lung adenocarcinoma

Author

Collisson, Eric A., Campbell, Joshua D., Brooks, Angela N., Berger, Alice H., Lee, William, Chmielecki, Juliann, Beer, David G., Cope, Leslie, Creighton, Chad J., Danilova, Ludmila, Ding, Li, Getz, Gad, Hammerman, Peter S., Hayes, D. Neil, Hernandez, Bryan, Herman, James G., Heymach, John V., Jurisica, Igor, Kucherlapati, Raju, Kwiatkowski, David, Ladanyi, Marc, Robertson, Gordon, Schultz, Nikolaus, Shen, Ronglai, Sinha, Rileen, Sougnez, Carrie, Tsao, Ming-Sound, Travis, William D., Weinstein, John N., Wigle, Dennis A., Wilkerson, Matthew D., Chu, Andy, Cherniack, Andrew D., Hadjipanayis, Angela, Rosenberg, Mara, Weisenberger, Daniel J., Laird, Peter W., Radenbaugh, Amie, Ma, Singer, Stuart, Joshua M., Byers, Lauren Averett, Baylin, Stephen B., Govindan, Ramaswamy, Meyerson, Matthew, Gabriel, Stacey B., Cibulskis, Kristian, Kim, Jaegil, Stewart, Chip, Lichtenstein, Lee, Lander, Eric S., Lawrence, Michael S., Kandoth, Cyriac, Fulton, Robert, Fulton, Lucinda L., McLellan, Michael D., Wilson, Richard K., Ye, Kai, Fronick, Catrina C., Maher, Christopher A., Miller, Christopher A., Wendl, Michael C., Cabanski, Christopher, Mardis, Elaine, Wheeler, David, Balasundaram, Miruna, Butterfield, Yaron S. N., Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Guin, Ranabir, Hirst, Carrie, Lee, Darlene, Li, Haiyan I., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Varhol, Richard, Robertson, A. Gordon, Wye, Natasja, Thiessen, Nina, Holt, Robert A., Jones, Steven J. M., Marra, Marco A., Imielinski, Marcin, Onofrio, Robert C., Hodis, Eran, Zack, Travis, Helman, Elena, Pedamallu, Chandra Sekhar, Mesirov, Jill, Saksena, Gordon, Schumacher, Steven E., Carter, Scott L., Garraway, Levi, Beroukhim, Rameen, Lee, Semin, Mahadeshwar, Harshad S., Pantazi, Angeliki, Protopopov, Alexei, Ren, Xiaojia, Seth, Sahil, Song, Xingzhi, Tang, Jiabin, Yang, Lixing, Zhang, Jianhua, Chen, Peng-Chieh, Parfenov, Michael, Xu, Andrew Wei, Santoso, Netty, Chin, Lynda, Park, Peter J., Hoadley, Katherine A., Auman, J. Todd, Meng, Shaowu, Shi, Yan, Buda, Elizabeth, Waring, Scot, Veluvolu, Umadevi, Tan, Donghui, Mieczkowski, Piotr A., Jones, Corbin D., Simons, Janae V., Soloway, Matthew G., Bodenheimer, Tom, Jefferys, Stuart R., Roach, Jeffrey, Hoyle, Alan P., Wu, Junyuan, Balu, Saianand, Singh, Darshan, Prins, Jan F., Marron, J. S., Parker, Joel S., Perou, Charles M., Liu, Jinze, Maglinte, Dennis T., Lai, Philip H., Bootwalla, Moiz S., Van Den Berg, David J., Triche, Timothy, Jr., Cho, Juok, DiCara, Daniel, Heiman, David, Lin, Pei, Mallard, William, Voet, Douglas, Zhang, Hailei, Zou, Lihua, Noble, Michael S., Gehlenborg, Nils, Thorvaldsdottir, Helga, Nazaire, Marc-Danie, Robinson, Jim, Aksoy, B. Arman, Ciriello, Giovanni, Taylor, Barry S., Dresdner, Gideon, Gao, Jianjiong, Gross, Benjamin, Seshan, Venkatraman E., Reva, Boris, Sumer, S. Onur, Weinhold, Nils, Sander, Chris, Zhu, Jingchun, Benz, Christopher C., Yau, Christina, Haussler, David, Spellman, Paul T., Kimes, Patrick K., Broom, Bradley M., Wang, Jing, Lu, Yiling, Diao, Lixia, Liu, Wenbin, Amos, Christopher I., Akbani, Rehan, Mills, Gordon B., Curley, Erin, Paulauskis, Joseph, Lau, Kevin, Morris, Scott, Shelton, Troy, Mallery, David, Gardner, Johanna, Penny, Robert, Saller, Charles, Tarvin, Katherine, Richards, William G., Cerfolio, Robert, Bryant, Ayesha, Raymond, Daniel P., Pennell, Nathan A., Farver, Carol, Czerwinski, Christine, Huelsenbeck-Dill, Lori, Iacocca, Mary, Petrelli, Nicholas, Rabeno, Brenda, Brown, Jennifer, Bauer, Thomas, Dolzhanskiy, Oleg, Potapova, Olga, Rotin, Daniil, Voronina, Olga, Nemirovich-Danchenko, Elena, Fedosenko, Konstantin V., Gal, Anthony, Behera, Madhusmita, Ramalingam, Suresh S., Sica, Gabriel, Flieder, Douglas, Boyd, Jeff, Weaver, JoEllen, Kohl, Bernard, Sandusky, George, Juhl, Hartmut, Duhig, Edwina, Illei, Peter, Gabrielson, Edward, Shin, James, Lee, Beverly, Rogers, Kristen, Trusty, Dante, Brock, Malcolm V., Williamson, Christina, Burks, Eric, Rieger-Christ, Kimberly, Holway, Antonia, Sullivan, Travis, Asiedu, Michael K., Kosari, Farhad, Rekhtman, Natasha, Zakowski, Maureen, Rusch, Valerie W., Zippile, Paul, Suh, James, Pass, Harvey, Goparaju, Chandra, Owusu-Sarpong, Yvonne, Bartlett, John M. S., Kodeeswaran, Sugy, Parfitt, Jeremy, Sekhon, Harmanjatinder, Albert, Monique, Eckman, John, Myers, Jerome B., Cheney, Richard, Morrison, Carl, Gaudioso, Carmelo, Borgia, Jeffrey A., Bonomi, Philip, Pool, Mark, Liptay, Michael J., Moiseenko, Fedor, Zaytseva, Irina, Dienemann, Hendrik, Meister, Michael, Schnabel, Philipp A., Muley, Thomas R., Peifer, Martin, Gomez-Fernandez, Carmen, Herbert, Lynn, Egea, Sophie, Huang, Mei, Thorne, Leigh B., Boice, Lori, Salazar, Ashley Hill, Funkhouser, William K., Rathmell, W. Kimryn, Dhir, Rajiv, Yousem, Samuel A., Dacic, Sanja, Schneider, Frank, Siegfried, Jill M., Hajek, Richard, Watson, Mark A., McDonald, Sandra, Meyers, Bryan, Clarke, Belinda, Yang, Ian A., Fong, Kwun M., Hunter, Lindy, Windsor, Morgan, Bowman, Rayleen V., Peters, Solange, Letovanec, Igor, Khan, Khurram Z., Jensen, Mark A., Snyder, Eric E., Srinivasan, Deepak, Kahn, Ari B., Baboud, Julien, Pot, David A., Shaw, Kenna R. Mills, Sheth, Margi, Davidsen, Tanja, Demchok, John A., Yang, Liming, Wang, Zhining, Tarnuzzer, Roy, Zenklusen, Jean Claude, Ozenberger, Bradley A., Sofia, Heidi J., Collisson, Eric A., Campbell, Joshua D., Brooks, Angela N., Berger, Alice H., Lee, William, Chmielecki, Juliann, Beer, David G., Cope, Leslie, Creighton, Chad J., Danilova, Ludmila, Ding, Li, Getz, Gad, Hammerman, Peter S., Hayes, D. Neil, Hernandez, Bryan, Herman, James G., Heymach, John V., Jurisica, Igor, Kucherlapati, Raju, Kwiatkowski, David, Ladanyi, Marc, Robertson, Gordon, Schultz, Nikolaus, Shen, Ronglai, Sinha, Rileen, Sougnez, Carrie, Tsao, Ming-Sound, Travis, William D., Weinstein, John N., Wigle, Dennis A., Wilkerson, Matthew D., Chu, Andy, Cherniack, Andrew D., Hadjipanayis, Angela, Rosenberg, Mara, Weisenberger, Daniel J., Laird, Peter W., Radenbaugh, Amie, Ma, Singer, Stuart, Joshua M., Byers, Lauren Averett, Baylin, Stephen B., Govindan, Ramaswamy, Meyerson, Matthew, Gabriel, Stacey B., Cibulskis, Kristian, Kim, Jaegil, Stewart, Chip, Lichtenstein, Lee, Lander, Eric S., Lawrence, Michael S., Kandoth, Cyriac, Fulton, Robert, Fulton, Lucinda L., McLellan, Michael D., Wilson, Richard K., Ye, Kai, Fronick, Catrina C., Maher, Christopher A., Miller, Christopher A., Wendl, Michael C., Cabanski, Christopher, Mardis, Elaine, Wheeler, David, Balasundaram, Miruna, Butterfield, Yaron S. N., Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Guin, Ranabir, Hirst, Carrie, Lee, Darlene, Li, Haiyan I., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Varhol, Richard, Robertson, A. Gordon, Wye, Natasja, Thiessen, Nina, Holt, Robert A., Jones, Steven J. M., Marra, Marco A., Imielinski, Marcin, Onofrio, Robert C., Hodis, Eran, Zack, Travis, Helman, Elena, Pedamallu, Chandra Sekhar, Mesirov, Jill, Saksena, Gordon, Schumacher, Steven E., Carter, Scott L., Garraway, Levi, Beroukhim, Rameen, Lee, Semin, Mahadeshwar, Harshad S., Pantazi, Angeliki, Protopopov, Alexei, Ren, Xiaojia, Seth, Sahil, Song, Xingzhi, Tang, Jiabin, Yang, Lixing, Zhang, Jianhua, Chen, Peng-Chieh, Parfenov, Michael, Xu, Andrew Wei, Santoso, Netty, Chin, Lynda, Park, Peter J., Hoadley, Katherine A., Auman, J. Todd, Meng, Shaowu, Shi, Yan, Buda, Elizabeth, Waring, Scot, Veluvolu, Umadevi, Tan, Donghui, Mieczkowski, Piotr A., Jones, Corbin D., Simons, Janae V., Soloway, Matthew G., Bodenheimer, Tom, Jefferys, Stuart R., Roach, Jeffrey, Hoyle, Alan P., Wu, Junyuan, Balu, Saianand, Singh, Darshan, Prins, Jan F., Marron, J. S., Parker, Joel S., Perou, Charles M., Liu, Jinze, Maglinte, Dennis T., Lai, Philip H., Bootwalla, Moiz S., Van Den Berg, David J., Triche, Timothy, Jr., Cho, Juok, DiCara, Daniel, Heiman, David, Lin, Pei, Mallard, William, Voet, Douglas, Zhang, Hailei, Zou, Lihua, Noble, Michael S., Gehlenborg, Nils, Thorvaldsdottir, Helga, Nazaire, Marc-Danie, Robinson, Jim, Aksoy, B. Arman, Ciriello, Giovanni, Taylor, Barry S., Dresdner, Gideon, Gao, Jianjiong, Gross, Benjamin, Seshan, Venkatraman E., Reva, Boris, Sumer, S. Onur, Weinhold, Nils, Sander, Chris, Zhu, Jingchun, Benz, Christopher C., Yau, Christina, Haussler, David, Spellman, Paul T., Kimes, Patrick K., Broom, Bradley M., Wang, Jing, Lu, Yiling, Diao, Lixia, Liu, Wenbin, Amos, Christopher I., Akbani, Rehan, Mills, Gordon B., Curley, Erin, Paulauskis, Joseph, Lau, Kevin, Morris, Scott, Shelton, Troy, Mallery, David, Gardner, Johanna, Penny, Robert, Saller, Charles, Tarvin, Katherine, Richards, William G., Cerfolio, Robert, Bryant, Ayesha, Raymond, Daniel P., Pennell, Nathan A., Farver, Carol, Czerwinski, Christine, Huelsenbeck-Dill, Lori, Iacocca, Mary, Petrelli, Nicholas, Rabeno, Brenda, Brown, Jennifer, Bauer, Thomas, Dolzhanskiy, Oleg, Potapova, Olga, Rotin, Daniil, Voronina, Olga, Nemirovich-Danchenko, Elena, Fedosenko, Konstantin V., Gal, Anthony, Behera, Madhusmita, Ramalingam, Suresh S., Sica, Gabriel, Flieder, Douglas, Boyd, Jeff, Weaver, JoEllen, Kohl, Bernard, Sandusky, George, Juhl, Hartmut, Duhig, Edwina, Illei, Peter, Gabrielson, Edward, Shin, James, Lee, Beverly, Rogers, Kristen, Trusty, Dante, Brock, Malcolm V., Williamson, Christina, Burks, Eric, Rieger-Christ, Kimberly, Holway, Antonia, Sullivan, Travis, Asiedu, Michael K., Kosari, Farhad, Rekhtman, Natasha, Zakowski, Maureen, Rusch, Valerie W., Zippile, Paul, Suh, James, Pass, Harvey, Goparaju, Chandra, Owusu-Sarpong, Yvonne, Bartlett, John M. S., Kodeeswaran, Sugy, Parfitt, Jeremy, Sekhon, Harmanjatinder, Albert, Monique, Eckman, John, Myers, Jerome B., Cheney, Richard, Morrison, Carl, Gaudioso, Carmelo, Borgia, Jeffrey A., Bonomi, Philip, Pool, Mark, Liptay, Michael J., Moiseenko, Fedor, Zaytseva, Irina, Dienemann, Hendrik, Meister, Michael, Schnabel, Philipp A., Muley, Thomas R., Peifer, Martin, Gomez-Fernandez, Carmen, Herbert, Lynn, Egea, Sophie, Huang, Mei, Thorne, Leigh B., Boice, Lori, Salazar, Ashley Hill, Funkhouser, William K., Rathmell, W. Kimryn, Dhir, Rajiv, Yousem, Samuel A., Dacic, Sanja, Schneider, Frank, Siegfried, Jill M., Hajek, Richard, Watson, Mark A., McDonald, Sandra, Meyers, Bryan, Clarke, Belinda, Yang, Ian A., Fong, Kwun M., Hunter, Lindy, Windsor, Morgan, Bowman, Rayleen V., Peters, Solange, Letovanec, Igor, Khan, Khurram Z., Jensen, Mark A., Snyder, Eric E., Srinivasan, Deepak, Kahn, Ari B., Baboud, Julien, Pot, David A., Shaw, Kenna R. Mills, Sheth, Margi, Davidsen, Tanja, Demchok, John A., Yang, Liming, Wang, Zhining, Tarnuzzer, Roy, Zenklusen, Jean Claude, Ozenberger, Bradley A., and Sofia, Heidi J.

Abstract

Adenocarcinoma of the lung is the leading cause of cancer death worldwide. Here we report molecular profiling of 230 resected lung adenocarcinomas using messenger RNA, microRNA and DNA sequencing integrated with copy number, methylation and proteomic analyses. High rates of somatic mutation were seen(mean 8.9 mutations per megabase). Eighteen genes were statistically significantly mutated, including RIT1 activating mutations and newly described loss-of-function MGA mutations which are mutually exclusive with focal MYC amplification. EGFR mutations were more frequent in female patients, whereas mutations in RBM10 were more common in males. Aberrations in NF1, MET, ERBB2 and RIT1 occurred in 13% of cases and were enriched in samples otherwise lacking an activated oncogene, suggesting a driver role for these events in certain tumours. DNA and mRNA sequence from the same tumour highlighted splicing alterations driven by somatic genomic changes, including exon 14 skipping in MET mRNA in 4% of cases. MAPK and PI(3)K pathway activity, when measured at the protein level, was explained by known mutations in only a fraction of cases, suggesting additional, unexplained mechanisms of pathway activation. These data establish a foundation for classification and further investigations of lung adenocarcinoma molecular pathogenesis.

Published
2014

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