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48 results on '"Parfenov, Michael"'

1. On Decompositions of H-holomorphic functions into quaternionic power series

Author

Parfenov, Michael

Subjects
Mathematics - Complex Variables, 30G35
Abstract

Based on the full similarity in algebraic properties and differentiation rules between quaternionic (H-) holomorphic and complex (C-) holomorphic functions, we assume that there exists one holistic notion of a holomorphic function that has a H-representation in the case of quaternions and a C-representation in the case of complex variables. We get the essential definitions and criteria for a quaternionic power series convergence, adapting complex analogues to the quaternion case. It is established that the power series expansions of any holomorphic function in C- and H-representations are similar and converge with identical convergence radiuses. We define a H-analytic function and prove that every H-holomorphic function is H-analytic. Some examples of power series expansions are given., Comment: 22 pages

Published
2024

2. On the notion of a quaternionic holomorphic function

Author

Parfenov, Michael

Subjects
Mathematics - Complex Variables, 30G35
Abstract

A physically more adequate definition of a quaternionic holomorphic (H-holomorphic) function of one quaternionic variable compared to known ones and a quaternionic generalization of Cauchy-Riemann's equations are presented. At that a class of introduced H-holomorphic functions consists of those quaternionic functions whose left and right derivatives become equal after the transition to 3D space. The presented theory demonstrates a complete similarity of the algebraic properties and differentiation rules between the classes of H-holomorphic and ordinary complex holomorphic functions, including the fact that quaternionic multiplication of the H-holomorphic functions behaves as commutative and the fact that each H-holomorphic function can be created from its complex holomorphic analogue by replacing a complex variable by a quaternion one. A fairly large number of detailed examples are given to illustrate the presented theory efficiency., Comment: 16 pages

Published
2024

4. Genomic analyses implicate noncoding de novo variants in congenital heart disease

Author

Richter, Felix, Morton, Sarah U, Kim, Seong Won, Kitaygorodsky, Alexander, Wasson, Lauren K, Chen, Kathleen M, Zhou, Jian, Qi, Hongjian, Patel, Nihir, DePalma, Steven R, Parfenov, Michael, Homsy, Jason, Gorham, Joshua M, Manheimer, Kathryn B, Velinder, Matthew, Farrell, Andrew, Marth, Gabor, Schadt, Eric E, Kaltman, Jonathan R, Newburger, Jane W, Giardini, Alessandro, Goldmuntz, Elizabeth, Brueckner, Martina, Kim, Richard, Porter, George A, Bernstein, Daniel, Chung, Wendy K, Srivastava, Deepak, Tristani-Firouzi, Martin, Troyanskaya, Olga G, Dickel, Diane E, Shen, Yufeng, Seidman, Jonathan G, Seidman, Christine E, and Gelb, Bruce D

Subjects
Biological Sciences, Genetics, Congenital Structural Anomalies, Heart Disease, Pediatric, Human Genome, Cardiovascular, Aetiology, 2.1 Biological and endogenous factors, Adolescent, Adult, Animals, Female, Genetic Predisposition to Disease, Genetic Variation, Genomics, Heart, Heart Defects, Congenital, Humans, Male, Mice, Middle Aged, Open Reading Frames, RNA, Untranslated, RNA-Binding Proteins, Transcription, Genetic, Young Adult, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

A genetic etiology is identified for one-third of patients with congenital heart disease (CHD), with 8% of cases attributable to coding de novo variants (DNVs). To assess the contribution of noncoding DNVs to CHD, we compared genome sequences from 749 CHD probands and their parents with those from 1,611 unaffected trios. Neural network prediction of noncoding DNV transcriptional impact identified a burden of DNVs in individuals with CHD (n = 2,238 DNVs) compared to controls (n = 4,177; P = 8.7 × 10-4). Independent analyses of enhancers showed an excess of DNVs in associated genes (27 genes versus 3.7 expected, P = 1 × 10-5). We observed significant overlap between these transcription-based approaches (odds ratio (OR) = 2.5, 95% confidence interval (CI) 1.1-5.0, P = 5.4 × 10-3). CHD DNVs altered transcription levels in 5 of 31 enhancers assayed. Finally, we observed a DNV burden in RNA-binding-protein regulatory sites (OR = 1.13, 95% CI 1.1-1.2, P = 8.8 × 10-5). Our findings demonstrate an enrichment of potentially disruptive regulatory noncoding DNVs in a fraction of CHD at least as high as that observed for damaging coding DNVs.

Published
2020

5. Robust identification of deletions in exome and genome sequence data based on clustering of Mendelian errors

Author

Manheimer, Kathryn B, Patel, Nihir, Richter, Felix, Gorham, Joshua, Tai, Angela C, Homsy, Jason, Boskovski, Marko T, Parfenov, Michael, Goldmuntz, Elizabeth, Chung, Wendy K, Brueckner, Martina, Tristani‐Firouzi, Martin, Srivastava, Deepak, Seidman, Jonathan G, Seidman, Christine E, Gelb, Bruce D, and Sharp, Andrew J

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Pediatric, Biotechnology, Human Genome, Chromosome Mapping, DNA Copy Number Variations, DNA Mutational Analysis, Exome, Female, Genome, Human, Heart Defects, Congenital, Humans, Male, Sequence Deletion, Exome Sequencing, Whole Genome Sequencing, copy number variant identification, UPD, whole exome sequencing, whole genome sequencing, Clinical Sciences, Genetics & Heredity, Clinical sciences
Abstract

Multiple tools have been developed to identify copy number variants (CNVs) from whole exome (WES) and whole genome sequencing (WGS) data. Current tools such as XHMM for WES and CNVnator for WGS identify CNVs based on changes in read depth. For WGS, other methods to identify CNVs include utilizing discordant read pairs and split reads and genome-wide local assembly with tools such as Lumpy and SvABA, respectively. Here, we introduce a new method to identify deletion CNVs from WES and WGS trio data based on the clustering of Mendelian errors (MEs). Using our Mendelian Error Method (MEM), we identified 127 deletions (inherited and de novo) in 2,601 WES trios from the Pediatric Cardiac Genomics Consortium, with a validation rate of 88% by digital droplet PCR. MEM identified additional de novo deletions compared with XHMM, and a significant enrichment of 15q11.2 deletions compared with controls. In addition, MEM identified eight cases of uniparental disomy, sample switches, and DNA contamination. We applied MEM to WGS data from the Genome In A Bottle Ashkenazi trio and identified deletions with 97% specificity. MEM provides a robust, computationally inexpensive method for identifying deletions, and an orthogonal approach for verifying deletions called by other tools.

Published
2018

6. Integrated genomic and molecular characterization of cervical cancer

Author

Burk, Robert D, Chen, Zigui, Saller, Charles, Tarvin, Katherine, Carvalho, Andre L, Scapulatempo-Neto, Cristovam, Silveira, Henrique C, Fregnani, José H, Creighton, Chad J, Anderson, Matthew L, Castro, Patricia, Wang, Sophia S, Yau, Christina, Benz, Christopher, Robertson, A Gordon, Mungall, Karen, Lim, Lynette, Bowlby, Reanne, Sadeghi, Sara, Brooks, Denise, Sipahimalani, Payal, Mar, Richard, Ally, Adrian, Clarke, Amanda, Mungall, Andrew J, Tam, Angela, Lee, Darlene, Chuah, Eric, Schein, Jacqueline E, Tse, Kane, Kasaian, Katayoon, Ma, Yussanne, Marra, Marco A, Mayo, Michael, Balasundaram, Miruna, Thiessen, Nina, Dhalla, Noreen, Carlsen, Rebecca, Moore, Richard A, Holt, Robert A, Jones, Steven JM, Wong, Tina, Pantazi, Angeliki, Parfenov, Michael, Kucherlapati, Raju, Hadjipanayis, Angela, Seidman, Jonathan, Kucherlapati, Melanie, Ren, Xiaojia, Xu, Andrew W, Yang, Lixing, Park, Peter J, Lee, Semin, Rabeno, Brenda, Huelsenbeck-Dill, Lori, Borowsky, Mark, Cadungog, Mark, Iacocca, Mary, Petrelli, Nicholas, Swanson, Patricia, Ojesina, Akinyemi I, Le, Xuan, Sandusky, George, Adebamowo, Sally N, Akeredolu, Teniola, Adebamowo, Clement, Reynolds, Sheila M, Shmulevich, Ilya, Shelton, Candace, Crain, Daniel, Mallery, David, Curley, Erin, Gardner, Johanna, Penny, Robert, Morris, Scott, Shelton, Troy, Liu, Jia, Lolla, Laxmi, Chudamani, Sudha, Wu, Ye, Birrer, Michael, McLellan, Michael D, Bailey, Matthew H, Miller, Christopher A, Wyczalkowski, Matthew A, Fulton, Robert S, Fronick, Catrina C, Lu, Charles, Mardis, Elaine R, Appelbaum, Elizabeth L, Schmidt, Heather K, Fulton, Lucinda A, Cordes, Matthew G, Li, Tiandao, Ding, Li, Wilson, Richard K, Rader, Janet S, Behmaram, Behnaz, Uyar, Denise, and Bradley, William

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Immunology, Cervical Cancer, Cancer, Clinical Research, Human Genome, Sexually Transmitted Infections, Biotechnology, Genetics, 2.1 Biological and endogenous factors, Aetiology, APOBEC-1 Deaminase, Adenocarcinoma, B7-H1 Antigen, Carcinoma, Squamous Cell, Caspase 8, DNA-Binding Proteins, Female, Genomics, HLA-A Antigens, Human papillomavirus 16, Humans, Keratins, Mitogen-Activated Protein Kinase Kinases, Molecular Targeted Therapy, Mutation, Nuclear Proteins, PTEN Phosphohydrolase, Phosphatidylinositol 3-Kinases, Programmed Cell Death 1 Ligand 2 Protein, Protein Serine-Threonine Kinases, Proteomics, Proto-Oncogene Proteins p21(ras), RNA, Long Noncoding, Receptor, ErbB-3, Receptor, Transforming Growth Factor-beta Type II, Receptors, Transforming Growth Factor beta, Signal Transduction, Transcription Factors, Uterine Cervical Neoplasms, Virus Integration, Cancer Genome Atlas Research Network, Albert Einstein College of Medicine, Analytical Biological Services, Barretos Cancer Hospital, Baylor College of Medicine, Beckman Research Institute of City of Hope, Buck Institute for Research on Aging, Canada's Michael Smith Genome Sciences Centre, Harvard Medical School, Helen F. Graham Cancer Center &Research Institute at Christiana Care Health Services, HudsonAlpha Institute for Biotechnology, ILSbio, LLC, Indiana University School of Medicine, Institute of Human Virology, Institute for Systems Biology, International Genomics Consortium, Leidos Biomedical, Massachusetts General Hospital, McDonnell Genome Institute at Washington University, Medical College of Wisconsin, Medical University of South Carolina, Memorial Sloan Kettering Cancer Center, Montefiore Medical Center, NantOmics, National Cancer Institute, National Hospital, Abuja, Nigeria, National Human Genome Research Institute, National Institute of Environmental Health Sciences, National Institute on Deafness &Other Communication Disorders, Ontario Tumour Bank, London Health Sciences Centre, Ontario Tumour Bank, Ontario Institute for Cancer Research, Ontario Tumour Bank, The Ottawa Hospital, Oregon Health &Science University, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, SRA International, St Joseph's Candler Health System, Eli &Edythe L. Broad Institute of Massachusetts Institute of Technology &Harvard University, Research Institute at Nationwide Children's Hospital, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, University of Bergen, University of Texas MD Anderson Cancer Center, University of Abuja Teaching Hospital, University of Alabama at Birmingham, University of California, Irvine, University of California Santa Cruz, University of Kansas Medical Center, University of Lausanne, University of New Mexico Health Sciences Center, University of North Carolina at Chapel Hill, University of Oklahoma Health Sciences Center, University of Pittsburgh, University of São Paulo, Ribeir ão Preto Medical School, University of Southern California, University of Washington, University of Wisconsin School of Medicine &Public Health, Van Andel Research Institute, Washington University in St Louis, Receptor, erbB-3, General Science & Technology
Abstract

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

Published
2017

7. 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 SN, Carlsen, Rebecca, Cheng, Dean, Chu, Andy, Dhalla, Noreen, Guin, Ranabir, Holt, Robert A, Jones, Steven JM, Lee, Darlene, Li, Haiyan I, Marra, Marco A, Mayo, Michael, Moore, Richard A, Mungall, Andrew J, Gordon Robertson, 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, Hong Fan, You, Liu, Jinze, Wang, Kai, Todd Auman, J, Balu, Saianand, Bodenheimer, Thomas, Buda, Elizabeth, Neil Hayes, D, Hoadley, Katherine A, Hoyle, Alan P, Jefferys, Stuart R, Jones, Corbin D, Kimes, Patrick K, Liu, Yufeng, Marron, JS, 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, Sekhar Pedamallu, Chandra, and Saksena, Gordon

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Oncology and Carcinogenesis, Human Genome, Biotechnology, Dental/Oral and Craniofacial Disease, Cancer, 2.1 Biological and endogenous factors, Aetiology, Good Health and Well Being, Carcinoma, Squamous Cell, DNA Copy Number Variations, DNA, Neoplasm, Female, Gene Expression Regulation, Neoplastic, Genome, Human, Genomics, Head and Neck Neoplasms, Humans, Male, Molecular Targeted Therapy, Mutation, Oncogenes, RNA, Neoplasm, Signal Transduction, Squamous Cell Carcinoma of Head and Neck, Transcription Factors, Cancer Genome Atlas Network, General Science & Technology
Abstract

The Cancer Genome Atlas profiled 279 head and neck squamous cell carcinomas (HNSCCs) to provide a comprehensive landscape of somatic genomic alterations. Here we show that human-papillomavirus-associated tumours are dominated by helical domain mutations of the oncogene PIK3CA, novel alterations involving loss of TRAF3, and amplification of the cell cycle gene E2F1. Smoking-related HNSCCs demonstrate near universal loss-of-function TP53 mutations and CDKN2A inactivation with frequent copy number alterations including amplification of 3q26/28 and 11q13/22. A subgroup of oral cavity tumours with favourable clinical outcomes displayed infrequent copy number alterations in conjunction with activating mutations of HRAS or PIK3CA, coupled with inactivating mutations of CASP8, NOTCH1 and TP53. Other distinct subgroups contained loss-of-function alterations of the chromatin modifier NSD1, WNT pathway genes AJUBA and FAT1, and activation of oxidative stress factor NFE2L2, mainly in laryngeal tumours. Therapeutic candidate alterations were identified in most HNSCCs.

Published
2015

8. A gene-centric strategy for identifying disease-causing rare variants in dilated cardiomyopathy

Author

Horvat, Claire, Johnson, Renee, Lam, Lien, Munro, Jacob, Mazzarotto, Francesco, Roberts, Angharad M., Herman, Daniel S., Parfenov, Michael, Haghighi, Alireza, McDonough, Barbara, DePalma, Steven R., Keogh, Anne M., Macdonald, Peter S., Hayward, Christopher S., Roberts, Amy, Barton, Paul J.R., Felkin, Leanne E., Giannoulatou, Eleni, Cook, Stuart A., Seidman, J.G., Seidman, Christine E., and Fatkin, Diane

Published
2019
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9. Characterization of HPV and host genome interactions in primary head and neck cancers

Author

Parfenov, Michael, Pedamallu, Chandra Sekhar, Gehlenborg, Nils, Freeman, Samuel S, Danilova, Ludmila, Bristow, Christopher A, Lee, Semin, Hadjipanayis, Angela G, Ivanova, Elena V, Wilkerson, Matthew D, Protopopov, Alexei, Yang, Lixing, Seth, Sahil, Song, Xingzhi, Tang, Jiabin, Ren, Xiaojia, Zhang, Jianhua, Pantazi, Angeliki, Santoso, Netty, Xu, Andrew W, Mahadeshwar, Harshad, Wheeler, David A, Haddad, Robert I, Jung, Joonil, Ojesina, Akinyemi I, Issaeva, Natalia, Yarbrough, Wendell G, Hayes, D Neil, Grandis, Jennifer R, El-Naggar, Adel K, Meyerson, Matthew, Park, Peter J, Chin, Lynda, Seidman, JG, Hammerman, Peter S, Kucherlapati, Raju, Ally, Adrian, Balasundaram, Miruna, Birol, Inanc, Bowlby, Reanne, Butterfield, Yaron SN, Carlsen, Rebecca, Cheng, Dean, Chu, Andy, Dhalla, Noreen, Guin, Ranabir, Holt, Robert A, Jones, Steven JM, Lee, Darlene, Li, Haiyan I, Marra, Marco A, Mayo, Michael, Moore, Richard A, Mungall, Andrew J, Robertson, A Gordon, Schein, Jacqueline E, Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Wong, Tina, Mahadeshwar, Harshad S, Haseley, Psalm, Zeng, Dong, Bristow, Christopher, Hadjipanayis, Angela, Seidman, Jonathan, 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, J Todd, Balu, Saianand, Bodenheimer, Tom, Buda, Elizabeth, Hoadley, Katherine A, and Hoyle, Alan P

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Bioinformatics and Computational Biology, Genetics, Oncology and Carcinogenesis, Rare Diseases, Human Genome, Sexually Transmitted Infections, Cervical Cancer, Infectious Diseases, Dental/Oral and Craniofacial Disease, HIV/AIDS, Cancer, 2.2 Factors relating to the physical environment, Aetiology, 2.1 Biological and endogenous factors, Infection, Base Sequence, DNA Methylation, Gene Expression Regulation, Neoplastic, Genes, Neoplasm, Genome, Human, Head and Neck Neoplasms, Host-Pathogen Interactions, Humans, Molecular Sequence Data, Papillomaviridae, Virus Integration, cancer, head and neck, papilloma virus, genome rearrangement, integration sites, Cancer Genome Atlas Network
Abstract

Previous studies have established that a subset of head and neck tumors contains human papillomavirus (HPV) sequences and that HPV-driven head and neck cancers display distinct biological and clinical features. HPV is known to drive cancer by the actions of the E6 and E7 oncoproteins, but the molecular architecture of HPV infection and its interaction with the host genome in head and neck cancers have not been comprehensively described. We profiled a cohort of 279 head and neck cancers with next generation RNA and DNA sequencing and show that 35 (12.5%) tumors displayed evidence of high-risk HPV types 16, 33, or 35. Twenty-five cases had integration of the viral genome into one or more locations in the human genome with statistical enrichment for genic regions. Integrations had a marked impact on the human genome and were associated with alterations in DNA copy number, mRNA transcript abundance and splicing, and both inter- and intrachromosomal rearrangements. Many of these events involved genes with documented roles in cancer. Cancers with integrated vs. nonintegrated HPV displayed different patterns of DNA methylation and both human and viral gene expressions. Together, these data provide insight into the mechanisms by which HPV interacts with the human genome beyond expression of viral oncoproteins and suggest that specific integration events are an integral component of viral oncogenesis.

Published
2014

10. 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, A Gordon, Sipahimalani, Payal, Cherniack, Andrew, Getz, Gad, Liu, Yingchun, Noble, Michael S, Pedamallu, Chandra, Sougnez, Carrie, Taylor-Weiner, Amaro, Akbani, Rehan, Lee, Ju-Seog, Liu, Wenbin, Mills, Gordon B, Yang, Da, Zhang, Wei, Pantazi, Angeliki, Parfenov, Michael, Gulley, Margaret, Piazuelo, M Blanca, 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 SN, Carlsen, Rebecca, Chu, Justin, Chuah, Eric, Chun, Hye-Jung E, Clarke, Amanda, Dhalla, Noreen, Guin, Ranabir, Holt, Robert A, Jones, Steven JM, Lee, Darlene, Li, Haiyan A, Lim, Emilia, Ma, Yussanne, Marra, Marco A, Mayo, Michael, Moore, Richard A, Mungall, Karen L, Ming Nip, Ka, and Schein, Jacqueline E

Subjects
Genetics, Digestive Diseases, Genetic Testing, Human Genome, Rare Diseases, Cancer, Good Health and Well Being, Adenocarcinoma, Female, Gene Expression Regulation, Neoplastic, Genome, Human, Herpesvirus 4, Human, Humans, Male, Mutation, Proteome, Stomach Neoplasms, Cancer Genome Atlas Research Network, General Science & Technology
Abstract

Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and clinical characteristics has been complicated by histological and aetiological heterogeneity. Here we describe a comprehensive molecular evaluation of 295 primary gastric adenocarcinomas as part of The Cancer Genome Atlas (TCGA) project. We propose a molecular classification dividing gastric cancer into four subtypes: tumours positive for Epstein-Barr virus, which display recurrent PIK3CA mutations, extreme DNA hypermethylation, and amplification of JAK2, CD274 (also known as PD-L1) and PDCD1LG2 (also known as PD-L2); microsatellite unstable tumours, which show elevated mutation rates, including mutations of genes encoding targetable oncogenic signalling proteins; genomically stable tumours, which are enriched for the diffuse histological variant and mutations of RHOA or fusions involving RHO-family GTPase-activating proteins; and tumours with chromosomal instability, which show marked aneuploidy and focal amplification of receptor tyrosine kinases. Identification of these subtypes provides a roadmap for patient stratification and trials of targeted therapies.

Published
2014

11. Loss of FHL1 induces an age-dependent skeletal muscle myopathy associated with myofibrillar and intermyofibrillar disorganization in mice

Author

Domenighetti, Andrea A, Chu, Pao-Hsien, Wu, Tongbin, Sheikh, Farah, Gokhin, David S, Guo, Ling T, Cui, Ziyou, Peter, Angela K, Christodoulou, Danos C, Parfenov, Michael G, Gorham, Joshua M, Li, Daniel Y, Banerjee, Indroneal, Lai, Xianyin, Witzmann, Frank A, Seidman, Christine E, Seidman, Jonathan G, Gomes, Aldrin V, Shelton, G Diane, Lieber, Richard L, and Chen, Ju

Subjects
Biological Sciences, Genetics, Muscular Dystrophy, Rare Diseases, Pediatric, 2.1 Biological and endogenous factors, Musculoskeletal, Age Factors, Animals, Cell Differentiation, Female, Humans, Intracellular Signaling Peptides and Proteins, LIM Domain Proteins, Male, Mice, Mice, Transgenic, Motor Activity, Muscle Proteins, Muscle, Skeletal, Muscular Dystrophies, Muscular Dystrophy, Emery-Dreifuss, Myoblasts, Skeletal, Myofibrils, Medical and Health Sciences, Genetics & Heredity
Abstract

Recent human genetic studies have provided evidences that sporadic or inherited missense mutations in four-and-a-half LIM domain protein 1 (FHL1), resulting in alterations in FHL1 protein expression, are associated with rare congenital myopathies, including reducing body myopathy and Emery-Dreifuss muscular dystrophy. However, it remains to be clarified whether mutations in FHL1 cause skeletal muscle remodeling owing to gain- or loss of FHL1 function. In this study, we used FHL1-null mice lacking global FHL1 expression to evaluate loss-of-function effects on skeletal muscle homeostasis. Histological and functional analyses of soleus, tibialis anterior and sternohyoideus muscles demonstrated that FHL1-null mice develop an age-dependent myopathy associated with myofibrillar and intermyofibrillar (mitochondrial and sarcoplasmic reticulum) disorganization, impaired muscle oxidative capacity and increased autophagic activity. A longitudinal study established decreased survival rates in FHL1-null mice, associated with age-dependent impairment of muscle contractile function and a significantly lower exercise capacity. Analysis of primary myoblasts isolated from FHL1-null muscles demonstrated early muscle fiber differentiation and maturation defects, which could be rescued by re-expression of the FHL1A isoform, highlighting that FHL1A is necessary for proper muscle fiber differentiation and maturation in vitro. Overall, our data show that loss of FHL1 function leads to myopathy in vivo and suggest that loss of function of FHL1 may be one of the mechanisms underlying muscle dystrophy in patients with FHL1 mutations.

Published
2014

12. The Cancer Genome Atlas Pan-Cancer analysis project

Author

Chang, Kyle, Creighton, Chad J, Davis, Caleb, Donehower, Lawrence, Drummond, Jennifer, Wheeler, David, Ally, Adrian, Balasundaram, Miruna, Birol, Inanc, Butterfield, Yaron SN, Chu, Andy, Chuah, Eric, Chun, Hye-Jung E, Dhalla, Noreen, Guin, Ranabir, Hirst, Martin, Hirst, Carrie, Holt, Robert A, Jones, Steven JM, Lee, Darlene, Li, Haiyan I, Marra, Marco A, Mayo, Michael, Moore, Richard A, Mungall, Andrew J, Robertson, A Gordon, Schein, Jacqueline E, Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Varhol, Richard J, Beroukhim, Rameen, Bhatt, Ami S, Brooks, Angela N, Cherniack, Andrew D, Freeman, Samuel S, Gabriel, Stacey B, Helman, Elena, Jung, Joonil, Meyerson, Matthew, Ojesina, Akinyemi I, Pedamallu, Chandra Sekhar, Saksena, Gordon, Schumacher, Steven E, Tabak, Barbara, Zack, Travis, Lander, Eric S, Bristow, Christopher A, Hadjipanayis, Angela, Haseley, Psalm, Kucherlapati, Raju, Lee, Semin, Lee, Eunjung, Luquette, Lovelace J, Mahadeshwar, Harshad S, Pantazi, Angeliki, Parfenov, Michael, Park, Peter J, Protopopov, Alexei, Ren, Xiaojia, Santoso, Netty, Seidman, Jonathan, Seth, Sahil, Song, Xingzhi, Tang, Jiabin, Xi, Ruibin, Xu, Andrew W, Yang, Lixing, Zeng, Dong, Auman, J Todd, Balu, Saianand, Buda, Elizabeth, Fan, Cheng, Hoadley, Katherine A, Jones, Corbin D, Meng, Shaowu, Mieczkowski, Piotr A, Parker, Joel S, Perou, Charles M, Roach, Jeffrey, Shi, Yan, Silva, Grace O, Tan, Donghui, Veluvolu, Umadevi, Waring, Scot, Wilkerson, Matthew D, Wu, Junyuan, Zhao, Wei, Bodenheimer, Tom, Hayes, D Neil, Hoyle, Alan P, Jeffreys, Stuart R, Mose, Lisle E, Simons, Janae V, Soloway, Mathew G, Baylin, Stephen B, Berman, Benjamin P, Bootwalla, Moiz S, Danilova, Ludmila, and Herman, James G

Subjects
Biological Sciences, Genetics, Cancer, Human Genome, Rare Diseases, Good Health and Well Being, Gene Expression Profiling, Genome, Humans, Neoplasms, Cancer Genome Atlas Research Network, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile.

Published
2013

13. De novo mutations in histone-modifying genes in congenital heart disease.

Author

Zaidi, Samir, Choi, Murim, Wakimoto, Hiroko, Ma, Lijiang, Jiang, Jianming, Overton, John, Romano-Adesman, Angela, Bjornson, Robert, Breitbart, Roger, Brown, Kerry, Carriero, Nicholas, Cheung, Yee, Deanfield, John, DePalma, Steve, Fakhro, Khalid, Glessner, Joseph, Hakonarson, Hakon, Italia, Michael, Kaltman, Jonathan, Kaski, Juan, Kim, Richard, Kline, Jennie, Lee, Teresa, Leipzig, Jeremy, Lopez, Alexander, Mane, Shrikant, Mitchell, Laura, Newburger, Jane, Parfenov, Michael, Peer, Itsik, Porter, George, Roberts, Amy, Sachidanandam, Ravi, Subramanian, Sailakshmi, Tikhonova, Irina, Wang, Wei, Warburton, Dorothy, White, Peter, Williams, Ismee, Zhao, Hongyu, Seidman, Jonathan, Brueckner, Martina, Chung, Wendy, Gelb, Bruce, Goldmuntz, Elizabeth, Seidman, Christine, Lifton, Richard, Seiden, Howard, State, Matthew, and Sanders, Stephan

Subjects
Adult, Case-Control Studies, Child, Chromatin, DNA Mutational Analysis, Enhancer Elements, Genetic, Exome, Female, Genes, Developmental, Heart Diseases, Histones, Humans, Lysine, Male, Methylation, Mutation, Odds Ratio, Promoter Regions, Genetic
Abstract

Congenital heart disease (CHD) is the most frequent birth defect, affecting 0.8% of live births. Many cases occur sporadically and impair reproductive fitness, suggesting a role for de novo mutations. Here we compare the incidence of de novo mutations in 362 severe CHD cases and 264 controls by analysing exome sequencing of parent-offspring trios. CHD cases show a significant excess of protein-altering de novo mutations in genes expressed in the developing heart, with an odds ratio of 7.5 for damaging (premature termination, frameshift, splice site) mutations. Similar odds ratios are seen across the main classes of severe CHD. We find a marked excess of de novo mutations in genes involved in the production, removal or reading of histone 3 lysine 4 (H3K4) methylation, or ubiquitination of H2BK120, which is required for H3K4 methylation. There are also two de novo mutations in SMAD2, which regulates H3K27 methylation in the embryonic left-right organizer. The combination of both activating (H3K4 methylation) and inactivating (H3K27 methylation) chromatin marks characterizes poised promoters and enhancers, which regulate expression of key developmental genes. These findings implicate de novo point mutations in several hundreds of genes that collectively contribute to approximately 10% of severe CHD.

Published
2013

14. Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma

Author

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

Published
2017
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15. Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

Author

Anjum, Samreen, Arachchi, Harindra, Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Barnett, Gene, Baylin, Stephen, Bell, Sue, Benz, Christopher, Bir, Natalie, Black, Keith L., Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bristow, Christopher A., Butterfield, Yaron S.N., Chen, Qing-Rong, Chin, Lynda, Cho, Juok, Chuah, Eric, Chudamani, Sudha, Coetzee, Simon G., Cohen, Mark L., Colman, Howard, Couce, Marta, D’Angelo, Fulvio, Davidsen, Tanja, Davis, Amy, Demchok, John A., Devine, Karen, Ding, Li, Duell, Rebecca, Elder, J. Bradley, Eschbacher, Jennifer M., Fehrenbach, Ashley, Ferguson, Martin, Frazer, Scott, Fuller, Gregory, Fulop, Jordonna, Gabriel, Stacey B., Garofano, Luciano, Gastier-Foster, Julie M., Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Giannini, Caterina, Gibson, William J., Hadjipanayis, Angela, Hayes, D. Neil, Heiman, David I., Hermes, Beth, Hilty, Joe, Hoadley, Katherine A., Hoyle, Alan P., Huang, Mei, Jefferys, Stuart R., Jones, Corbin D., Jones, Steven J.M., Ju, Zhenlin, Kastl, Alison, Kendler, Ady, Kim, Jaegil, Kucherlapati, Raju, Lai, Phillip H., Lawrence, Michael S., Lee, Semin, Leraas, Kristen M., Lichtenberg, Tara M., Lin, Pei, Liu, Yuexin, Liu, Jia, Ljubimova, Julia Y., Lu, Yiling, Ma, Yussanne, Maglinte, Dennis T., Mahadeshwar, Harshad S., Marra, Marco A., McGraw, Mary, McPherson, Christopher, Meng, Shaowu, Mieczkowski, Piotr A., Miller, C. Ryan, Mills, Gordon B., Moore, Richard A., Mose, Lisle E., Mungall, Andrew J., Naresh, Rashi, Naska, Theresa, Neder, Luciano, Noble, Michael S., Noss, Ardene, O’Neill, Brian Patrick, Ostrom, Quinn T., Palmer, Cheryl, Pantazi, Angeliki, Parfenov, Michael, Park, Peter J., Parker, Joel S., Perou, Charles M., Pierson, Christopher R., Pihl, Todd, Protopopov, Alexei, Radenbaugh, Amie, Ramirez, Nilsa C., Rathmell, W. Kimryn, Ren, Xiaojia, Roach, Jeffrey, Robertson, A. Gordon, Saksena, Gordon, Schein, Jacqueline E., Schumacher, Steven E., Seidman, Jonathan, Senecal, Kelly, Seth, Sahil, Shen, Hui, Shi, Yan, Shih, Juliann, Shimmel, Kristen, Sicotte, Hugues, Sifri, Suzanne, Silva, Tiago, Simons, Janae V., Singh, Rosy, Skelly, Tara, Sloan, Andrew E., Sofia, Heidi J., Soloway, Matthew G., Song, Xingzhi, Sougnez, Carrie, Souza, Camila, Staugaitis, Susan M., Sun, Huandong, Sun, Charlie, Tan, Donghui, Tang, Jiabin, Tang, Yufang, Thorne, Leigh, Trevisan, Felipe Amstalden, Triche, Timothy, Van Den Berg, David J., Veluvolu, Umadevi, Voet, Doug, Wan, Yunhu, Wang, Zhining, Warnick, Ronald, Weinstein, John N., Weisenberger, Daniel J., Wilkerson, Matthew D., Williams, Felicia, Wise, Lisa, Wolinsky, Yingli, Wu, Junyuan, Xu, Andrew W., Yang, Lixing, Yang, Liming, Zack, Travis I., Zenklusen, Jean C., Zhang, Jianhua, Zhang, Wei, Zhang, Jiashan, Zmuda, Erik, Ceccarelli, Michele, Barthel, Floris P., Malta, Tathiane M., Sabedot, Thais S., Salama, Sofie R., Murray, Bradley A., Morozova, Olena, Newton, Yulia, Pagnotta, Stefano M., Wang, Jiguang, Manyam, Ganiraju, Zoppoli, Pietro, Ling, Shiyun, Rao, Arjun A., Grifford, Mia, Cherniack, Andrew D., Zhang, Hailei, Poisson, Laila, Carlotti, Carlos Gilberto, Jr., Tirapelli, Daniela Pretti da Cunha, Rao, Arvind, Mikkelsen, Tom, Lau, Ching C., Yung, W.K. Alfred, Rabadan, Raul, Huse, Jason, Brat, Daniel J., Lehman, Norman L., Barnholtz-Sloan, Jill S., Zheng, Siyuan, Hess, Kenneth, Rao, Ganesh, Meyerson, Matthew, Beroukhim, Rameen, Cooper, Lee, Akbani, Rehan, Wrensch, Margaret, Haussler, David, Aldape, Kenneth D., Laird, Peter W., Gutmann, David H., Noushmehr, Houtan, Iavarone, Antonio, and Verhaak, Roel G.W.

Published
2016
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16. The Molecular Taxonomy of Primary Prostate Cancer

Author

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

Published
2015
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17. Genomic Classification of Cutaneous Melanoma

Author

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

Published
2015
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18. 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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19. Integrated Genomic Characterization of Papillary Thyroid Carcinoma

Author

Agrawal, Nishant, Akbani, Rehan, Aksoy, B. Arman, Ally, Adrian, Arachchi, Harindra, Asa, Sylvia L., Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Baylin, Stephen B., Behera, Madhusmita, Bernard, Brady, Beroukhim, Rameen, Bishop, Justin A., Black, Aaron D., Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bowlby, Reanne, Bristow, Christopher A., Brookens, Robin, Brooks, Denise, Bryant, Robert, Buda, Elizabeth, Butterfield, Yaron S.N., Carling, Tobias, Carlsen, Rebecca, Carter, Scott L., Carty, Sally E., Chan, Timothy A., Chen, Amy Y., Cherniack, Andrew D., Cheung, Dorothy, Chin, Lynda, Cho, Juok, Chu, Andy, Chuah, Eric, Cibulskis, Kristian, Ciriello, Giovanni, Clarke, Amanda, Clayman, Gary L., Cope, Leslie, Copland, John A., Covington, Kyle, Danilova, Ludmila, Davidsen, Tanja, Demchok, John A., DiCara, Daniel, Dhalla, Noreen, Dhir, Rajiv, Dookran, Sheliann S., Dresdner, Gideon, Eldridge, Jonathan, Eley, Greg, El-Naggar, Adel K., Eng, Stephanie, Fagin, James A., Fennell, Timothy, Ferris, Robert L., Fisher, Sheila, Frazer, Scott, Frick, Jessica, Gabriel, Stacey B., Ganly, Ian, Gao, Jianjiong, Garraway, Levi A., Gastier-Foster, Julie M., Getz, Gad, Gehlenborg, Nils, Ghossein, Ronald, Gibbs, Richard A., Giordano, Thomas J., Gomez-Hernandez, Karen, Grimsby, Jonna, Gross, Benjamin, Guin, Ranabir, Hadjipanayis, Angela, Harper, Hollie A., Hayes, D. Neil, Heiman, David I., Herman, James G., Hoadley, Katherine A., Hofree, Matan, Holt, Robert A., Hoyle, Alan P., Huang, Franklin W., Huang, Mei, Hutter, Carolyn M., Ideker, Trey, Iype, Lisa, Jacobsen, Anders, Jefferys, Stuart R., Jones, Corbin D., Jones, Steven J.M., Kasaian, Katayoon, Kebebew, Electron, Khuri, Fadlo R., Kim, Jaegil, Kramer, Roger, Kreisberg, Richard, Kucherlapati, Raju, Kwiatkowski, David J., Ladanyi, Marc, Lai, Phillip H., Laird, Peter W., Lander, Eric, Lawrence, Michael S., Lee, Darlene, Lee, Eunjung, Lee, Semin, Lee, William, Leraas, Kristen M., Lichtenberg, Tara M., Lichtenstein, Lee, Lin, Pei, Ling, Shiyun, Liu, Jinze, Liu, Wenbin, Liu, Yingchun, LiVolsi, Virginia A., Lu, Yiling, Ma, Yussanne, Mahadeshwar, Harshad S., Marra, Marco A., Mayo, Michael, McFadden, David G., Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Miller, Michael, Mills, Gordon, Moore, Richard A., Mose, Lisle E., Mungall, Andrew J., Murray, Bradley A., Nikiforov, Yuri E., Noble, Michael S., Ojesina, Akinyemi I., Owonikoko, Taofeek K., Ozenberger, Bradley A., Pantazi, Angeliki, Parfenov, Michael, Park, Peter J., Parker, Joel S., Paull, Evan O., Pedamallu, Chandra Sekhar, Perou, Charles M., Prins, Jan F., Protopopov, Alexei, Ramalingam, Suresh S., Ramirez, Nilsa C., Ramirez, Ricardo, Raphael, Benjamin J., Rathmell, W. Kimryn, Ren, Xiaojia, Reynolds, Sheila M., Rheinbay, Esther, Ringel, Matthew D., Rivera, Michael, Roach, Jeffrey, Robertson, A. Gordon, Rosenberg, Mara W., Rosenthal, Matthew, Sadeghi, Sara, Saksena, Gordon, Sander, Chris, Santoso, Netty, Schein, Jacqueline E., Schultz, Nikolaus, Schumacher, Steven E., Seethala, Raja R., Seidman, Jonathan, Senbabaoglu, Yasin, Seth, Sahil, Sharpe, Samantha, Shaw, Kenna R. Mills, Shen, John P., Shen, Ronglai, Sherman, Steven, Sheth, Margi, Shi, Yan, Shmulevich, Ilya, Sica, Gabriel L., Simons, Janae V., Sinha, Rileen, Sipahimalani, Payal, Smallridge, Robert C., Sofia, Heidi J., Soloway, Matthew G., Song, Xingzhi, Sougnez, Carrie, Stewart, Chip, Stojanov, Petar, Stuart, Joshua M., Sumer, S. Onur, Sun, Yichao, Tabak, Barbara, Tam, Angela, Tan, Donghui, Tang, Jiabin, Tarnuzzer, Roy, Taylor, Barry S., Thiessen, Nina, Thorne, Leigh, Thorsson, Vésteinn, Tuttle, R. Michael, Umbricht, Christopher B., Van Den Berg, David J., Vandin, Fabio, Veluvolu, Umadevi, Verhaak, Roel G.W., Vinco, Michelle, Voet, Doug, Walter, Vonn, Wang, Zhining, Waring, Scot, Weinberger, Paul M., Weinhold, Nils, Weinstein, John N., Weisenberger, Daniel J., Wheeler, David, Wilkerson, Matthew D., Wilson, Jocelyn, Williams, Michelle, Winer, Daniel A., Wise, Lisa, Wu, Junyuan, Xi, Liu, Xu, Andrew W., Yang, Liming, Yang, Lixing, Zack, Travis I., Zeiger, Martha A., Zeng, Dong, Zenklusen, Jean Claude, Zhao, Ni, Zhang, Hailei, Zhang, Jianhua, Zhang, Jiashan (Julia), Zhang, Wei, Zmuda, Erik, and Zou, Lihua

Published
2014
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20. The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma

Author

Creighton, Chad J., Davis, Caleb F., Morgan, Margaret, Gunaratne, Preethi H., Donehower, Lawrence A., Kaipparettu, Benny A., Wheeler, David A., Gibbs, Richard A., Signoretti, Sabina, Cherniack, Andrew D., Robertson, A. Gordon, Chu, Andy, Choueiri, Toni K., Henske, Elizabeth P., Kwiatkowski, David J., Reuter, Victor, Hsieh, James J., Hakimi, A. Ari, Tickoo, Satish K., Ricketts, Christopher, Linehan, W. Marston, Schmidt, Laura S., Gordenin, Dmitry A., Bhanot, Gyan, Seiler, Michael, Tamboli, Pheroze, Rathmell, W. Kimryn, Fahey, Catherine C., Hacker, Kathryn E., Smith, Angela B., Wallen, Eric M., Shen, Hui, Laird, Peter W., Shuch, Brian, Muzny, Donna, Buhay, Christian, Wang, Min, Chao, Hsu, Dahdouli, Mike, Xi, Liu, Kakkar, Nipun, Reid, Jeffrey G., Downs, Brittany, Drummond, Jennifer, Morton, Donna, Doddapaneni, Harsha, Lewis, Lora, English, Adam, Meng, Qingchang, Kovar, Christie, Wang, Qiaoyan, Hale, Walker, Hawes, Alicia, Kalra, Divya, Walker, Kimberly, Murray, Bradley A., Sougnez, Carrie, Saksena, Gordon, Carter, Scott L., Schumacher, Steven E., Tabak, Barbara, Zack, Travis I., Getz, Gad, Beroukhim, Rameen, Gabriel, Stacey B., Meyerson, Matthew, Ally, Adrian, Balasundaram, Miruna, Birol, Inanc, Brooks, Denise, Butterfield, Yaron S.N., Chuah, Eric, Clarke, Amanda, Dhalla, Noreen, Guin, Ranabir, Holt, Robert A., Kasaian, Katayoon, Lee, Darlene, Li, Haiyan I., Lim, Emilia, Ma, Yussanne, Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Wong, Tina, Jones, Steven J.M., Marra, Marco A., Auman, J. Todd, Tan, Donghui, Meng, Shaowu, Jones, Corbin D., Hoadley, Katherine A., Mieczkowski, Piotr A., Mose, Lisle E., Jefferys, Stuart R., Roach, Jeffrey, Veluvolu, Umadevi, Wilkerson, Matthew D., Waring, Scot, Buda, Elizabeth, Wu, Junyuan, Bodenheimer, Tom, Hoyle, Alan P., Simons, Janae V., Soloway, Mathew G., Balu, Saianand, Parker, Joel S., Hayes, D. Neil, Perou, Charles M., Weisenberger, Daniel J., Bootwalla, Moiz S., Triche, Timothy, Jr., Lai, Phillip H., Van Den Berg, David J., Baylin, Stephen B., Chen, Fengju, Coarfa, Cristian, Noble, Michael S., DiCara, Daniel, Zhang, Hailei, Cho, Juok, Heiman, David I., Gehlenborg, Nils, Voet, Doug, Lin, Pei, Frazer, Scott, Stojanov, Petar, Liu, Yingchun, Zou, Lihua, Kim, Jaegil, Lawrence, Michael S., Chin, Lynda, Yang, Lixing, Seth, Sahil, Bristow, Christopher A., Protopopov, Alexei, Song, Xingzhi, Zhang, Jianhua, Pantazi, Angeliki, Hadjipanayis, Angela, Lee, Eunjung, Luquette, Lovelace J., Lee, Semin, Parfenov, Michael, Santoso, Netty, Seidman, Jonathan, Xu, Andrew W., Kucherlapati, Raju, Park, Peter J., Kang, Hyojin, Lee, Junehawk, Roberts, Steven A., Klimczak, Leszek J., Fargo, David, Lang, Martin, Choi, Yoon-La, Kim, Sang Cheol, Lee, June-Koo, Park, Woong-Yang, Wang, Wenyi, Fan, Yu, Ahn, Jaeil, Akbani, Rehan, Weinstein, John N., Haussler, David, Ma, Singer, Radenbaugh, Amie, Zhul, Jingchun, Biehl, Michael, Lichtenberg, Tara M., Zmuda, Erik, Black, Aaron D., Hanf, Benjamin, Ramirez, Nilsa C., Wise, Lisa, Bowen, Jay, Leraas, Kristen M., Hall, Tracy M., Gastier-Foster, Julie M., Kaelin, William G., Thorne, Leigh, Boice, Lori, Huang, Mei, Vocke, Cathy, Peterson, James, Worrell, Robert, Merino, Maria, Czerniak, Bogdan A., Aldape, Kenneth D., Wood, Christopher G., Spellman, Paul T., Atkins, Michael B., Cheville, John, Thompson, R. Houston, Jensen, Mark A., Pihl, Todd, Wan, Yunhu, Ayala, Brenda, Baboud, Julien, Velaga, Sudhakar, Walton, Jessica, Liu, Jia, Chudamani, Sudha, Wu, Ye, Sheth, Margi, Mills Shaw, Kenna R., Demchok, John A., Davidsen, Tanja, Yang, Liming, Wang, Zhining, Tarnuzzer, Roy W., Zhang, Jiashan, Eley, Greg, Felau, Ina, Zenklusen, Jean Claude, Hutter, Carolyn M., Guyer, Mark S., Ozenberger, Bradley A., Sofia, Heidi J., and Ricketts, Christopher J.

Published
2014
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21. Characterization of HPV and host genome interactions in primary head and neck cancers

Author

Cancer Genome Atlas Network, Parfenov, Michael, Pedamallu, Chandra Sekhar, Gehlenborg, Nils, Freeman, Samuel S., Danilova, Ludmila, Bristow, Christopher A., Lee, Semin, Hadjipanayis, Angela G., Ivanova, Elena V., Wilkerson, Matthew D., Protopopov, Alexei, Yang, Lixing, Seth, Sahil, Song, Xingzhi, Tang, Jiabin, Ren, Xiaojia, Zhang, Jianhua, Pantazi, Angeliki, Santoso, Netty, Xu, Andrew W., Mahadeshwar, Harshad, Wheeler, David A., Haddad, Robert I., Jung, Joonil, Ojesina, Akinyemi I., Issaeva, Natalia, Yarbrough, Wendell G., Hayes, D. Neil, Grandis, Jennifer R., K. El-Naggar, Adel, Meyerson, Matthew, Park, Peter J., Chin, Lynda, Seidman, J. G., Hammerman, Peter S., and Kucherlapati, Raju

Published
2014

22. 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

23. A functional genomic approach to actionable gene fusions for precision oncology

Author

Li, Jun, primary, Lu, Hengyu, additional, Ng, Patrick Kwok-Shing, additional, Pantazi, Angeliki, additional, Ip, Carman Ka Man, additional, Jeong, Kang Jin, additional, Amador, Bianca, additional, Tran, Richard, additional, Tsang, Yiu Huen, additional, Yang, Lixing, additional, Song, Xingzhi, additional, Dogruluk, Turgut, additional, Ren, Xiaojia, additional, Hadjipanayis, Angela, additional, Bristow, Christopher A., additional, Lee, Semin, additional, Kucherlapati, Melanie, additional, Parfenov, Michael, additional, Tang, Jiabin, additional, Seth, Sahil, additional, Mahadeshwar, Harshad S., additional, Mojumdar, Kamalika, additional, Zeng, Dong, additional, Zhang, Jianhua, additional, Protopopov, Alexei, additional, Seidman, Jonathan G., additional, Creighton, Chad J., additional, Lu, Yiling, additional, Sahni, Nidhi, additional, Shaw, Kenna R., additional, Meric-Bernstam, Funda, additional, Futreal, Andrew, additional, Chin, Lynda, additional, Scott, Kenneth L., additional, Kucherlapati, Raju, additional, Mills, Gordon B., additional, and Liang, Han, additional

Published
2022
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24. 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., Neil Hayes, D., 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., Averett Byers, Lauren, Baylin, Stephen B., Govindan, Ramaswamy, Meyerson, Matthew, Rosenberg, Mara, Gabriel, Stacey B., Cibulskis, Kristian, Sougnez, Carrie, Kim, Jaegil, Stewart, Chip, Lichtenstein, Lee, Lander, Eric S., Lawrence, Michael S., Getz, Gad, 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, Ding, Li, Mardis, Elaine, Govindan, Ramaswamy, Creighton, Chad J., Wheeler, David, Balasundaram, Miruna, Butterfield, Yaron S. N., Carlsen, Rebecca, Chu, Andy, 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, Gordon Robertson, A., Wye, Natasja, Thiessen, Nina, Holt, Robert A., Jones, Steven J. M., Marra, Marco A., Campbell, Joshua D., Brooks, Angela N., Chmielecki, Juliann, Imielinski, Marcin, Onofrio, Robert C., Hodis, Eran, Zack, Travis, Sougnez, Carrie, Helman, Elena, Sekhar Pedamallu, Chandra, Mesirov, Jill, Cherniack, Andrew D., Saksena, Gordon, Schumacher, Steven E., Carter, Scott L., Hernandez, Bryan, Garraway, Levi, Beroukhim, Rameen, Gabriel, Stacey B., Getz, Gad, Meyerson, Matthew, Hadjipanayis, Angela, 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, Wei Xu, Andrew, Santoso, Netty, Chin, Lynda, Park, Peter J., Kucherlapati, Raju, Hoadley, Katherine A., Todd Auman, J., 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., Neil Hayes, D., Perou, Charles M., Liu, Jinze, Cope, Leslie, Danilova, Ludmila, Weisenberger, Daniel J., Maglinte, Dennis T., Lai, Philip H., Bootwalla, Moiz S., Van Den Berg, David J., Triche Jr, Timothy, Baylin, Stephen B., Laird, Peter W., Rosenberg, Mara, Chin, Lynda, Zhang, Jianhua, Cho, Juok, DiCara, Daniel, Heiman, David, Lin, Pei, Mallard, William, Voet, Douglas, Zhang, Hailei, Zou, Lihua, Noble, Michael S., Lawrence, Michael S., Saksena, Gordon, Gehlenborg, Nils, Thorvaldsdottir, Helga, Mesirov, Jill, Nazaire, Marc-Danie, Robinson, Jim, Getz, Gad, Lee, William, Arman Aksoy, B., Ciriello, Giovanni, Taylor, Barry S., Dresdner, Gideon, Gao, Jianjiong, Gross, Benjamin, Seshan, Venkatraman E., Ladanyi, Marc, Reva, Boris, Sinha, Rileen, Onur Sumer, S., Weinhold, Nils, Schultz, Nikolaus, Shen, Ronglai, Sander, Chris, Ng, Sam, Ma, Singer, Zhu, Jingchun, Radenbaugh, Amie, Stuart, Joshua M., Benz, Christopher C., Yau, Christina, Haussler, David, Spellman, Paul T., Wilkerson, Matthew D., Parker, Joel S., Hoadley, Katherine A., Kimes, Patrick K., Neil Hayes, D., Perou, Charles M., Broom, Bradley M., Wang, Jing, Lu, Yiling, Kwok Shing Ng, Patrick, Diao, Lixia, Averett Byers, Lauren, Liu, Wenbin, Heymach, John V., Amos, Christopher I., Weinstein, John N., 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, Huy Quoc Thinh, Dang, 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, Wigle, Dennis A., Asiedu, Michael K., Kosari, Farhad, Travis, William D., 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, Hill Salazar, Ashley, Funkhouser, William K., Kimryn Rathmell, W., 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., Mills Shaw, Kenna R., Sheth, Margi, Davidsen, Tanja, Demchok, John A., Yang, Liming, Wang, Zhining, Tarnuzzer, Roy, Claude Zenklusen, Jean, Ozenberger, Bradley A., Sofia, Heidi J., Travis, William D., Cheney, Richard, Clarke, Belinda, Dacic, Sanja, Duhig, Edwina, Funkhouser, William K., Illei, Peter, Farver, Carol, Rekhtman, Natasha, Sica, Gabriel, Suh, James, and Tsao, Ming-Sound

Published
2014
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25. 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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28. Genomic analyses implicate noncoding de novo variants in congenital heart disease

Author

Richter, Felix, Morton, Sarah U, Kim, Seong Won, Kitaygorodsky, Alexander, Wasson, Lauren K, Chen, Kathleen M, Zhou, Jian, Qi, Hongjian, Patel, Nihir, DePalma, Steven R, Parfenov, Michael, Homsy, Jason, Gorham, Joshua M, Manheimer, Kathryn B, Velinder, Matthew, Farrell, Andrew, Marth, Gabor, Schadt, Eric E, Kaltman, Jonathan R, Newburger, Jane W, Giardini, Alessandro, Goldmuntz, Elizabeth, Brueckner, Martina, Kim, Richard, Porter, George A, Bernstein, Daniel, Chung, Wendy K, Srivastava, Deepak, Tristani-Firouzi, Martin, Troyanskaya, Olga G, Dickel, Diane E, Shen, Yufeng, Seidman, Jonathan G, Seidman, Christine E, and Gelb, Bruce D

Subjects
Adult, Heart Defects, Congenital, Male, RNA, Untranslated, Adolescent, Transcription, Genetic, Cardiovascular, Medical and Health Sciences, Congenital, Mice, Open Reading Frames, Young Adult, Genetic, Genetics, 2.1 Biological and endogenous factors, Animals, Humans, Genetic Predisposition to Disease, Aetiology, Heart Defects, Pediatric, Human Genome, Untranslated, Genetic Variation, RNA-Binding Proteins, Heart, Genomics, Biological Sciences, Middle Aged, Heart Disease, Congenital Structural Anomalies, RNA, Female, Transcription, Developmental Biology
Abstract

A genetic etiology is identified for one-third of patients with congenital heart disease (CHD), with 8% of cases attributable to coding de novo variants (DNVs). To assess the contribution of noncoding DNVs to CHD, we compared genome sequences from 749 CHD probands and their parents with those from 1,611 unaffected trios. Neural network prediction of noncoding DNV transcriptional impact identified a burden of DNVs in individuals with CHD (n = 2,238 DNVs) compared to controls (n = 4,177; P = 8.7 × 10-4). Independent analyses of enhancers showed an excess of DNVs in associated genes (27 genes versus 3.7 expected, P = 1 × 10-5). We observed significant overlap between these transcription-based approaches (odds ratio (OR) = 2.5, 95% confidence interval (CI) 1.1-5.0, P = 5.4 × 10-3). CHD DNVs altered transcription levels in 5 of 31 enhancers assayed. Finally, we observed a DNV burden in RNA-binding-protein regulatory sites (OR = 1.13, 95% CI 1.1-1.2, P = 8.8 × 10-5). Our findings demonstrate an enrichment of potentially disruptive regulatory noncoding DNVs in a fraction of CHD at least as high as that observed for damaging coding DNVs.

Published
2019

29. Abstract 5206: Role of super-enhancers in HPV+ head and neck squamous cell carcinoma

Author

Zamuner, Fernando T., primary, Vorontsov, Ilya, additional, Flam, Emily, additional, Mukhina, Vera, additional, Danilova, Ludmila, additional, Ou, Tingting, additional, Stavrovskaya, Elena, additional, Guo, Theresa, additional, Windsor, Eric, additional, Kelley, Dylan Z., additional, Parfenov, Michael, additional, Considine, Michael, additional, Fertig, Elana J., additional, Favorov, Alexander, additional, and Gaykalova, Daria A., additional

Published
2019
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30. Robust identification of deletions in exome and genome sequence data based on clustering of Mendelian errors.

Author

Seidman, Jonathan, Seidman, Jonathan, Seidman, Christine, Gelb, Bruce, Sharp, Andrew, Manheimer, Kathryn, Patel, Nihir, Richter, Felix, Gorham, Joshua, Tai, Angela, Homsy, Jason, Boskovski, Marko, Parfenov, Michael, Goldmuntz, Elizabeth, Chung, Wendy, Brueckner, Martina, Tristani-Firouzi, Martin, Srivastava, Deepak, Seidman, Jonathan, Seidman, Jonathan, Seidman, Christine, Gelb, Bruce, Sharp, Andrew, Manheimer, Kathryn, Patel, Nihir, Richter, Felix, Gorham, Joshua, Tai, Angela, Homsy, Jason, Boskovski, Marko, Parfenov, Michael, Goldmuntz, Elizabeth, Chung, Wendy, Brueckner, Martina, Tristani-Firouzi, Martin, and Srivastava, Deepak

Abstract

Multiple tools have been developed to identify copy number variants (CNVs) from whole exome (WES) and whole genome sequencing (WGS) data. Current tools such as XHMM for WES and CNVnator for WGS identify CNVs based on changes in read depth. For WGS, other methods to identify CNVs include utilizing discordant read pairs and split reads and genome-wide local assembly with tools such as Lumpy and SvABA, respectively. Here, we introduce a new method to identify deletion CNVs from WES and WGS trio data based on the clustering of Mendelian errors (MEs). Using our Mendelian Error Method (MEM), we identified 127 deletions (inherited and de novo) in 2,601 WES trios from the Pediatric Cardiac Genomics Consortium, with a validation rate of 88% by digital droplet PCR. MEM identified additional de novo deletions compared with XHMM, and a significant enrichment of 15q11.2 deletions compared with controls. In addition, MEM identified eight cases of uniparental disomy, sample switches, and DNA contamination. We applied MEM to WGS data from the Genome In A Bottle Ashkenazi trio and identified deletions with 97% specificity. MEM provides a robust, computationally inexpensive method for identifying deletions, and an orthogonal approach for verifying deletions called by other tools.

Published
2018

33. The Molecular Taxonomy of Primary Prostate Cancer

Author

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

Abstract

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

Published
2017

34. Robust identification of deletions in exome and genome sequence data based on clustering of Mendelian errors

Author

Manheimer, Kathryn B., primary, Patel, Nihir, additional, Richter, Felix, additional, Gorham, Joshua, additional, Tai, Angela C., additional, Homsy, Jason, additional, Boskovski, Marko T., additional, Parfenov, Michael, additional, Goldmuntz, Elizabeth, additional, Chung, Wendy K., additional, Brueckner, Martina, additional, Tristani-Firouzi, Martin, additional, Srivastava, Deepak, additional, Seidman, Jonathan G., additional, Seidman, Christine E., additional, Gelb, Bruce D., additional, and Sharp, Andrew J., additional

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

Author

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

Published
2017
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37. Molecular profiling of dilated cardiomyopathy that progresses to heart failure

Author

Burke, Michael A., primary, Chang, Stephen, additional, Wakimoto, Hiroko, additional, Gorham, Joshua M., additional, Conner, David A., additional, Christodoulou, Danos C., additional, Parfenov, Michael G., additional, DePalma, Steve R., additional, Eminaga, Seda, additional, Konno, Tetsuo, additional, Seidman, Jonathan G., additional, and Seidman, Christine E., additional

Published
2016
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38. Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

Author

Ceccarelli, Michele, primary, Barthel, Floris P., additional, Malta, Tathiane M., additional, Sabedot, Thais S., additional, Salama, Sofie R., additional, Murray, Bradley A., additional, Morozova, Olena, additional, Newton, Yulia, additional, Radenbaugh, Amie, additional, Pagnotta, Stefano M., additional, Anjum, Samreen, additional, Wang, Jiguang, additional, Manyam, Ganiraju, additional, Zoppoli, Pietro, additional, Ling, Shiyun, additional, Rao, Arjun A., additional, Grifford, Mia, additional, Cherniack, Andrew D., additional, Zhang, Hailei, additional, Poisson, Laila, additional, Carlotti, Carlos Gilberto, additional, Tirapelli, Daniela Pretti da Cunha, additional, Rao, Arvind, additional, Mikkelsen, Tom, additional, Lau, Ching C., additional, Yung, W.K. Alfred, additional, Rabadan, Raul, additional, Huse, Jason, additional, Brat, Daniel J., additional, Lehman, Norman L., additional, Barnholtz-Sloan, Jill S., additional, Zheng, Siyuan, additional, Hess, Kenneth, additional, Rao, Ganesh, additional, Meyerson, Matthew, additional, Beroukhim, Rameen, additional, Cooper, Lee, additional, Akbani, Rehan, additional, Wrensch, Margaret, additional, Haussler, David, additional, Aldape, Kenneth D., additional, Laird, Peter W., additional, Gutmann, David H., additional, Noushmehr, Houtan, additional, Iavarone, Antonio, additional, Verhaak, Roel G.W., additional, Arachchi, Harindra, additional, Auman, J. Todd, additional, Balasundaram, Miruna, additional, Balu, Saianand, additional, Barnett, Gene, additional, Baylin, Stephen, additional, Bell, Sue, additional, Benz, Christopher, additional, Bir, Natalie, additional, Black, Keith L., additional, Bodenheimer, Tom, additional, Boice, Lori, additional, Bootwalla, Moiz S., additional, Bowen, Jay, additional, Bristow, Christopher A., additional, Butterfield, Yaron S.N., additional, Chen, Qing-Rong, additional, Chin, Lynda, additional, Cho, Juok, additional, Chuah, Eric, additional, Chudamani, Sudha, additional, Coetzee, Simon G., additional, Cohen, Mark L., additional, Colman, Howard, additional, Couce, Marta, additional, D’Angelo, Fulvio, additional, Davidsen, Tanja, additional, Davis, Amy, additional, Demchok, John A., additional, Devine, Karen, additional, Ding, Li, additional, Duell, Rebecca, additional, Elder, J. Bradley, additional, Eschbacher, Jennifer M., additional, Fehrenbach, Ashley, additional, Ferguson, Martin, additional, Frazer, Scott, additional, Fuller, Gregory, additional, Fulop, Jordonna, additional, Gabriel, Stacey B., additional, Garofano, Luciano, additional, Gastier-Foster, Julie M., additional, Gehlenborg, Nils, additional, Gerken, Mark, additional, Getz, Gad, additional, Giannini, Caterina, additional, Gibson, William J., additional, Hadjipanayis, Angela, additional, Hayes, D. Neil, additional, Heiman, David I., additional, Hermes, Beth, additional, Hilty, Joe, additional, Hoadley, Katherine A., additional, Hoyle, Alan P., additional, Huang, Mei, additional, Jefferys, Stuart R., additional, Jones, Corbin D., additional, Jones, Steven J.M., additional, Ju, Zhenlin, additional, Kastl, Alison, additional, Kendler, Ady, additional, Kim, Jaegil, additional, Kucherlapati, Raju, additional, Lai, Phillip H., additional, Lawrence, Michael S., additional, Lee, Semin, additional, Leraas, Kristen M., additional, Lichtenberg, Tara M., additional, Lin, Pei, additional, Liu, Yuexin, additional, Liu, Jia, additional, Ljubimova, Julia Y., additional, Lu, Yiling, additional, Ma, Yussanne, additional, Maglinte, Dennis T., additional, Mahadeshwar, Harshad S., additional, Marra, Marco A., additional, McGraw, Mary, additional, McPherson, Christopher, additional, Meng, Shaowu, additional, Mieczkowski, Piotr A., additional, Miller, C. Ryan, additional, Mills, Gordon B., additional, Moore, Richard A., additional, Mose, Lisle E., additional, Mungall, Andrew J., additional, Naresh, Rashi, additional, Naska, Theresa, additional, Neder, Luciano, additional, Noble, Michael S., additional, Noss, Ardene, additional, O’Neill, Brian Patrick, additional, Ostrom, Quinn T., additional, Palmer, Cheryl, additional, Pantazi, Angeliki, additional, Parfenov, Michael, additional, Park, Peter J., additional, Parker, Joel S., additional, Perou, Charles M., additional, Pierson, Christopher R., additional, Pihl, Todd, additional, Protopopov, Alexei, additional, Ramirez, Nilsa C., additional, Rathmell, W. Kimryn, additional, Ren, Xiaojia, additional, Roach, Jeffrey, additional, Robertson, A. Gordon, additional, Saksena, Gordon, additional, Schein, Jacqueline E., additional, Schumacher, Steven E., additional, Seidman, Jonathan, additional, Senecal, Kelly, additional, Seth, Sahil, additional, Shen, Hui, additional, Shi, Yan, additional, Shih, Juliann, additional, Shimmel, Kristen, additional, Sicotte, Hugues, additional, Sifri, Suzanne, additional, Silva, Tiago, additional, Simons, Janae V., additional, Singh, Rosy, additional, Skelly, Tara, additional, Sloan, Andrew E., additional, Sofia, Heidi J., additional, Soloway, Matthew G., additional, Song, Xingzhi, additional, Sougnez, Carrie, additional, Souza, Camila, additional, Staugaitis, Susan M., additional, Sun, Huandong, additional, Sun, Charlie, additional, Tan, Donghui, additional, Tang, Jiabin, additional, Tang, Yufang, additional, Thorne, Leigh, additional, Trevisan, Felipe Amstalden, additional, Triche, Timothy, additional, Van Den Berg, David J., additional, Veluvolu, Umadevi, additional, Voet, Doug, additional, Wan, Yunhu, additional, Wang, Zhining, additional, Warnick, Ronald, additional, Weinstein, John N., additional, Weisenberger, Daniel J., additional, Wilkerson, Matthew D., additional, Williams, Felicia, additional, Wise, Lisa, additional, Wolinsky, Yingli, additional, Wu, Junyuan, additional, Xu, Andrew W., additional, Yang, Lixing, additional, Yang, Liming, additional, Zack, Travis I., additional, Zenklusen, Jean C., additional, Zhang, Jianhua, additional, Zhang, Wei, additional, Zhang, Jiashan, additional, and Zmuda, Erik, additional

Published
2016
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39. Burden of Rare Sarcomere Gene Variants in the Framingham and Jackson Heart Study Cohorts

Author

Bick, Alexander G., Flannick, Jason, Ito, Kaoru, Cheng, Susan, Vasan, Ramachandran S., Parfenov, Michael G., Herman, Daniel S., DePalma, Steven R., Gupta, Namrata, Gabriel, Stacey B., Funke, Birgit H., Rehm, Heidi L., Benjamin, Emelia J., Aragam, Jayashri, Taylor, Herman A., Jr., Fox, Ervin R., Newton-Cheh, Christopher, Kathiresan, Sekar, O’Donnell, Christopher J., Wilson, James G., Altshuler, David M., Hirschhorn, Joel N., Seidman, J.G., and Seidman, Christine

Published
2012
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41. The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma

Author

Davis, Caleb F., primary, Ricketts, Christopher J., additional, Wang, Min, additional, Yang, Lixing, additional, Cherniack, Andrew D., additional, Shen, Hui, additional, Buhay, Christian, additional, Kang, Hyojin, additional, Kim, Sang Cheol, additional, Fahey, Catherine C., additional, Hacker, Kathryn E., additional, Bhanot, Gyan, additional, Gordenin, Dmitry A., additional, Chu, Andy, additional, Gunaratne, Preethi H., additional, Biehl, Michael, additional, Seth, Sahil, additional, Kaipparettu, Benny A., additional, Bristow, Christopher A., additional, Donehower, Lawrence A., additional, Wallen, Eric M., additional, Smith, Angela B., additional, Tickoo, Satish K., additional, Tamboli, Pheroze, additional, Reuter, Victor, additional, Schmidt, Laura S., additional, Hsieh, James J., additional, Choueiri, Toni K., additional, Hakimi, A. Ari, additional, Chin, Lynda, additional, Meyerson, Matthew, additional, Kucherlapati, Raju, additional, Park, Woong-Yang, additional, Robertson, A. Gordon, additional, Laird, Peter W., additional, Henske, Elizabeth P., additional, Kwiatkowski, David J., additional, Park, Peter J., additional, Morgan, Margaret, additional, Shuch, Brian, additional, Muzny, Donna, additional, Wheeler, David A., additional, Linehan, W. Marston, additional, Gibbs, Richard A., additional, Rathmell, W. Kimryn, additional, Creighton, Chad J., additional, Creighton, Chad J., additional, Davis, Caleb F., additional, Wheeler, David A., additional, Gibbs, Richard A., additional, Signoretti, Sabina, additional, Robertson, A. Gordon, additional, Henske, Elizabeth P., additional, Kwiatkowski, David J., additional, Ricketts, Christopher, additional, Linehan, W. Marston, additional, Seiler, Michael, additional, Rathmell, W. Kimryn, additional, Laird, Peter W., additional, Chao, Hsu, additional, Dahdouli, Mike, additional, Xi, Liu, additional, Kakkar, Nipun, additional, Reid, Jeffrey G., additional, Downs, Brittany, additional, Drummond, Jennifer, additional, Morton, Donna, additional, Doddapaneni, Harsha, additional, Lewis, Lora, additional, English, Adam, additional, Meng, Qingchang, additional, Kovar, Christie, additional, Wang, Qiaoyan, additional, Hale, Walker, additional, Hawes, Alicia, additional, Kalra, Divya, additional, Walker, Kimberly, additional, Murray, Bradley A., additional, Sougnez, Carrie, additional, Saksena, Gordon, additional, Carter, Scott L., additional, Schumacher, Steven E., additional, Tabak, Barbara, additional, Zack, Travis I., additional, Getz, Gad, additional, Beroukhim, Rameen, additional, Gabriel, Stacey B., additional, Ally, Adrian, additional, Balasundaram, Miruna, additional, Birol, Inanc, additional, Brooks, Denise, additional, Butterfield, Yaron S.N., additional, Chuah, Eric, additional, Clarke, Amanda, additional, Dhalla, Noreen, additional, Guin, Ranabir, additional, Holt, Robert A., additional, Kasaian, Katayoon, additional, Lee, Darlene, additional, Li, Haiyan I., additional, Lim, Emilia, additional, Ma, Yussanne, additional, Mayo, Michael, additional, Moore, Richard A., additional, Mungall, Andrew J., additional, Schein, Jacqueline E., additional, Sipahimalani, Payal, additional, Tam, Angela, additional, Thiessen, Nina, additional, Wong, Tina, additional, Jones, Steven J.M., additional, Marra, Marco A., additional, Auman, J. Todd, additional, Tan, Donghui, additional, Meng, Shaowu, additional, Jones, Corbin D., additional, Hoadley, Katherine A., additional, Mieczkowski, Piotr A., additional, Mose, Lisle E., additional, Jefferys, Stuart R., additional, Roach, Jeffrey, additional, Veluvolu, Umadevi, additional, Wilkerson, Matthew D., additional, Waring, Scot, additional, Buda, Elizabeth, additional, Wu, Junyuan, additional, Bodenheimer, Tom, additional, Hoyle, Alan P., additional, Simons, Janae V., additional, Soloway, Mathew G., additional, Balu, Saianand, additional, Parker, Joel S., additional, Hayes, D. Neil, additional, Perou, Charles M., additional, Weisenberger, Daniel J., additional, Bootwalla, Moiz S., additional, Triche, Timothy, additional, Lai, Phillip H., additional, Van Den Berg, David J., additional, Baylin, Stephen B., additional, Chen, Fengju, additional, Coarfa, Cristian, additional, Noble, Michael S., additional, DiCara, Daniel, additional, Zhang, Hailei, additional, Cho, Juok, additional, Heiman, David I., additional, Gehlenborg, Nils, additional, Voet, Doug, additional, Lin, Pei, additional, Frazer, Scott, additional, Stojanov, Petar, additional, Liu, Yingchun, additional, Zou, Lihua, additional, Kim, Jaegil, additional, Lawrence, Michael S., additional, Protopopov, Alexei, additional, Song, Xingzhi, additional, Zhang, Jianhua, additional, Pantazi, Angeliki, additional, Hadjipanayis, Angela, additional, Lee, Eunjung, additional, Luquette, Lovelace J., additional, Lee, Semin, additional, Parfenov, Michael, additional, Santoso, Netty, additional, Seidman, Jonathan, additional, Xu, Andrew W., additional, Park, Peter J., additional, Lee, Junehawk, additional, Roberts, Steven A., additional, Klimczak, Leszek J., additional, Fargo, David, additional, Lang, Martin, additional, Choi, Yoon-La, additional, Lee, June-Koo, additional, Wang, Wenyi, additional, Fan, Yu, additional, Ahn, Jaeil, additional, Akbani, Rehan, additional, Weinstein, John N., additional, Haussler, David, additional, Ma, Singer, additional, Radenbaugh, Amie, additional, Zhul, Jingchun, additional, Lichtenberg, Tara M., additional, Zmuda, Erik, additional, Black, Aaron D., additional, Hanf, Benjamin, additional, Ramirez, Nilsa C., additional, Wise, Lisa, additional, Bowen, Jay, additional, Leraas, Kristen M., additional, Hall, Tracy M., additional, Gastier-Foster, Julie M., additional, Kaelin, William G., additional, Thorne, Leigh, additional, Boice, Lori, additional, Huang, Mei, additional, Vocke, Cathy, additional, Peterson, James, additional, Worrell, Robert, additional, Merino, Maria, additional, Czerniak, Bogdan A., additional, Aldape, Kenneth D., additional, Wood, Christopher G., additional, Spellman, Paul T., additional, Atkins, Michael B., additional, Cheville, John, additional, Thompson, R. Houston, additional, Jensen, Mark A., additional, Pihl, Todd, additional, Wan, Yunhu, additional, Ayala, Brenda, additional, Baboud, Julien, additional, Velaga, Sudhakar, additional, Walton, Jessica, additional, Liu, Jia, additional, Chudamani, Sudha, additional, Wu, Ye, additional, Sheth, Margi, additional, Mills Shaw, Kenna R., additional, Demchok, John A., additional, Davidsen, Tanja, additional, Yang, Liming, additional, Wang, Zhining, additional, Tarnuzzer, Roy W., additional, Zhang, Jiashan, additional, Eley, Greg, additional, Felau, Ina, additional, Zenklusen, Jean Claude, additional, Hutter, Carolyn M., additional, Guyer, Mark S., additional, Ozenberger, Bradley A., additional, and Sofia, Heidi J., additional

Published
2014
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42. Increased Burden of Cardiovascular Disease in Carriers of APOL1 Genetic Variants

Author

Ito, Kaoru, primary, Bick, Alexander G., additional, Flannick, Jason, additional, Friedman, David J., additional, Genovese, Giulio, additional, Parfenov, Michael G., additional, DePalma, Steven R., additional, Gupta, Namrata, additional, Gabriel, Stacey B., additional, Taylor, Herman A., additional, Fox, Ervin R., additional, Newton-Cheh, Christopher, additional, Kathiresan, Sekar, additional, Hirschhorn, Joel N., additional, Altshuler, David M., additional, Pollak, Martin R., additional, Wilson, James G., additional, Seidman, J.G., additional, and Seidman, Christine, additional

Published
2014
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43. Loss of FHL1 induces an age-dependent skeletal muscle myopathy associated with myofibrillar and intermyofibrillar disorganization in mice

Author

Domenighetti, Andrea A., primary, Chu, Pao-Hsien, additional, Wu, Tongbin, additional, Sheikh, Farah, additional, Gokhin, David S., additional, Guo, Ling T., additional, Cui, Ziyou, additional, Peter, Angela K., additional, Christodoulou, Danos C., additional, Parfenov, Michael G., additional, Gorham, Joshua M., additional, Li, Daniel Y., additional, Banerjee, Indroneal, additional, Lai, Xianyin, additional, Witzmann, Frank A., additional, Seidman, Christine E., additional, Seidman, Jonathan G., additional, Gomes, Aldrin V., additional, Shelton, G. Diane, additional, Lieber, Richard L., additional, and Chen, Ju, additional

Published
2013
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44. 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, A. Gordon, Sipahimalani, Payal, Cherniack, Andrew, Getz, Gad, Liu, Yingchun, Noble, Michael S., Pedamallu, Chandra, Sougnez, Carrie, Taylor-Weiner, Amaro, Akbani, Rehan, Lee, Ju-Seog, Liu, Wenbin, Mills, Gordon B., Yang, Da, Zhang, Wei, Pantazi, Angeliki, Parfenov, Michael, Gulley, Margaret, Piazuelo, M. Blanca, 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, 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, Van Den Berg, David J., Baylin, Stephen B., Herman, James G., Murray, Bradley A., Askoy, B. Arman, Ciriello, Giovanni, Dresdner, Gideon, Gao, Jianjiong, Gross, Benjamin, Jacobsen, Anders, Lee, William, Ramirez, Ricardo, Sander, Chris, Senbabaoglu, Yasin, Sinha, Rileen, Sumer, S. Onur, Sun, Yichao, Thorsson, Vésteinn, Iype, Lisa, Kramer, Roger W., Kreisberg, Richard, Rovira, Hector, Tasman, Natalie, Ng, Santa Cruz Sam, 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, Smitry, Dolzhansky, Oleg, Rathmell, W. Kimryn, Brzezinski, Jakub, Ibbs, Matthew, Korski, Konstanty, Kycler, Witold, ŁaŸniak, 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, M. Constanza, 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

Abstract

Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and clinical characteristics has been complicated by histological and aetiological heterogeneity. Here we describe a comprehensive molecular evaluation of 295 primary gastric adenocarcinomas as part of The Cancer Genome Atlas (TCGA) project. We propose a molecular classification dividing gastric cancer into four subtypes: tumours positive for Epstein–Barr virus, which display recurrent PIK3CA mutations, extreme DNA hypermethylation, and amplification of JAK2, CD274 (also known as PD-L1) and PDCD1LG2 (also knownasPD-L2); microsatellite unstable tumours, which show elevated mutation rates, including mutations of genes encoding targetable oncogenic signalling proteins; genomically stable tumours, which are enriched for the diffuse histological variant and mutations of RHOA or fusions involving RHO-family GTPase-activating proteins; and tumours with chromosomal instability, which show marked aneuploidy and focal amplification of receptor tyrosine kinases. Identification of these subtypes provides a roadmap for patient stratification and trials of targeted therapies.

Published
2014
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45. Integrated genomic and molecular characterization of cervical cance

Author

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

46. Integrated genomic characterization of oesophageal carcinoma

Author

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

Subjects
3. Good health
Abstract

Oesophageal cancers are prominent worldwide; however, there are few targeted therapies and survival rates for these cancers remain dismal. Here we performed a comprehensive molecular analysis of 164 carcinomas of the oesophagus derived from Western and Eastern populations. Beyond known histopathological and epidemiologic distinctions, molecular features differentiated oesophageal squamous cell carcinomas from oesophageal adenocarcinomas. Oesophageal squamous cell carcinomas resembled squamous carcinomas of other organs more than they did oesophageal adenocarcinomas. Our analyses identified three molecular subclasses of oesophageal squamous cell carcinomas, but none showed evidence for an aetiological role of human papillomavirus. Squamous cell carcinomas showed frequent genomic amplifications of CCND1 and SOX2 and/or TP63, whereas ERBB2, VEGFA and GATA4 and GATA6 were more commonly amplified in adenocarcinomas. Oesophageal adenocarcinomas strongly resembled the chromosomally unstable variant of gastric adenocarcinoma, suggesting that these cancers could be considered a single disease entity. However, some molecular features, including DNA hypermethylation, occurred disproportionally in oesophageal adenocarcinomas. These data provide a framework to facilitate more rational categorization of these tumours and a foundation for new therapies.

47. A functional genomic approach to actionable gene fusions for precision oncology.

Author

Jun Li, Hengyu Lu, Kwok-Shing Ng, Patrick, Pantazi, Angeliki, Ka Man Ip, Carman, Kang Jin Jeong, Amador, Bianca, Tran, Richard, Yiu Huen Tsang, Lixing Yang, Xingzhi Song, Dogruluk, Turgut, Xiaojia Ren, Hadjipanayis, Angela, Bristow, Christopher A., Lee, Semin, Kucherlapati, Melanie, Parfenov, Michael, Jiabin Tang, and Seth, Sahil

Subjects
*GENE fusion, *ONCOLOGY, *TUMOR growth, *PHARMACOGENOMICS, *CELL survival, *DRUG target
Abstract

Fusion genes represent a class of attractive therapeutic targets. Thousands of fusion genes have been identified in patients with cancer, but the functional consequences and therapeutic implications of most of these remain largely unknown. Here, we develop a functional genomic approach that consists of efficient fusion reconstruction and sensitive cell viability and drug response assays. Applying this approach, we characterize ~100 fusion genes detected in patient samples of The Cancer Genome Atlas, revealing a notable fraction of low-frequency fusions with activating effects on tumor growth. Focusing on those in the RTK-RAS pathway, we identify a number of activating fusions that can markedly affect sensitivity to relevant drugs. Last, we propose an integrated, level-of-evidence classification system to prioritize gene fusions systematically. Our study reiterates the urgent clinical need to incorporate similar functional genomic approaches to characterize gene fusions, thereby maximizing the utility of gene fusions for precision oncology. [ABSTRACT FROM AUTHOR]

Published
2022
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48. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Author

Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR, Cooper LA, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, Akbani R, Huse JT, Ciriello G, Poisson LM, Barnholtz-Sloan JS, Berger MS, Brennan C, Colen RR, Colman H, Flanders AE, Giannini C, Grifford M, Iavarone A, Jain R, Joseph I, Kim J, Kasaian K, Mikkelsen T, Murray BA, O'Neill BP, Pachter L, Parsons DW, Sougnez C, Sulman EP, Vandenberg SR, Van Meir EG, von Deimling A, Zhang H, Crain D, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton T, Sherman M, Yena P, Black A, Bowen J, Dicostanzo K, Gastier-Foster J, Leraas KM, Lichtenberg TM, Pierson CR, Ramirez NC, Taylor C, Weaver S, Wise L, Zmuda E, Davidsen T, Demchok JA, Eley G, Ferguson ML, Hutter CM, Mills Shaw KR, Ozenberger BA, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Ayala B, Baboud J, Chudamani S, Jensen MA, Liu J, Pihl T, Raman R, Wan Y, Wu Y, Ally A, Auman JT, Balasundaram M, Balu S, Baylin SB, Beroukhim R, Bootwalla MS, Bowlby R, Bristow CA, Brooks D, Butterfield Y, Carlsen R, Carter S, Chin L, Chu A, Chuah E, Cibulskis K, Clarke A, Coetzee SG, Dhalla N, Fennell T, Fisher S, Gabriel S, Getz G, Gibbs R, Guin R, Hadjipanayis A, Hayes DN, Hinoue T, Hoadley K, Holt RA, Hoyle AP, Jefferys SR, Jones S, Jones CD, Kucherlapati R, Lai PH, Lander E, Lee S, Lichtenstein L, Ma Y, Maglinte DT, Mahadeshwar HS, Marra MA, Mayo M, Meng S, Meyerson ML, Mieczkowski PA, Moore RA, Mose LE, Mungall AJ, Pantazi A, Parfenov M, Park PJ, Parker JS, Perou CM, Protopopov A, Ren X, Roach J, Sabedot TS, Schein J, Schumacher SE, Seidman JG, Seth S, Shen H, Simons JV, Sipahimalani P, Soloway MG, Song X, Sun H, Tabak B, Tam A, Tan D, Tang J, Thiessen N, Triche T Jr, Van Den Berg DJ, Veluvolu U, Waring S, Weisenberger DJ, Wilkerson MD, Wong T, Wu J, Xi L, Xu AW, Yang L, Zack TI, Zhang J, Aksoy BA, Arachchi H, Benz C, Bernard B, Carlin D, Cho J, DiCara D, Frazer S, Fuller GN, Gao J, Gehlenborg N, Haussler D, Heiman DI, Iype L, Jacobsen A, Ju Z, Katzman S, Kim H, Knijnenburg T, Kreisberg RB, Lawrence MS, Lee W, Leinonen K, Lin P, Ling S, Liu W, Liu Y, Liu Y, Lu Y, Mills G, Ng S, Noble MS, Paull E, Rao A, Reynolds S, Saksena G, Sanborn Z, Sander C, Schultz N, Senbabaoglu Y, Shen R, Shmulevich I, Sinha R, Stuart J, Sumer SO, Sun Y, Tasman N, Taylor BS, Voet D, Weinhold N, Weinstein JN, Yang D, Yoshihara K, Zheng S, Zhang W, Zou L, Abel T, Sadeghi S, Cohen ML, Eschbacher J, Hattab EM, Raghunathan A, Schniederjan MJ, Aziz D, Barnett G, Barrett W, Bigner DD, Boice L, Brewer C, Calatozzolo C, Campos B, Carlotti CG Jr, Chan TA, Cuppini L, Curley E, Cuzzubbo S, Devine K, DiMeco F, Duell R, Elder JB, Fehrenbach A, Finocchiaro G, Friedman W, Fulop J, Gardner J, Hermes B, Herold-Mende C, Jungk C, Kendler A, Lehman NL, Lipp E, Liu O, Mandt R, McGraw M, Mclendon R, McPherson C, Neder L, Nguyen P, Noss A, Nunziata R, Ostrom QT, Palmer C, Perin A, Pollo B, Potapov A, Potapova O, Rathmell WK, Rotin D, Scarpace L, Schilero C, Senecal K, Shimmel K, Shurkhay V, Sifri S, Singh R, Sloan AE, Smolenski K, Staugaitis SM, Steele R, Thorne L, Tirapelli DP, Unterberg A, Vallurupalli M, Wang Y, Warnick R, Williams F, Wolinsky Y, Bell S, Rosenberg M, Stewart C, Huang F, Grimsby JL, Radenbaugh AJ, and Zhang J

Subjects
Adolescent, Adult, Aged, Chromosomes, Human, Pair 1, Chromosomes, Human, Pair 19, Cluster Analysis, Female, Glioblastoma genetics, Glioma metabolism, Glioma mortality, Humans, Kaplan-Meier Estimate, Male, Middle Aged, Neoplasm Grading, Proportional Hazards Models, Sequence Analysis, DNA, Signal Transduction, DNA, Neoplasm analysis, Genes, p53, Glioma genetics, Mutation
Abstract

Background: Diffuse 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., Methods: We 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., Results: Unsupervised 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., Conclusions: The 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
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