Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions (2009)
Sos, Martin L., Michel, Kathrin, Zander, Thomas, Weiss, Jonathan, Frommolt, Peter, Peifer, Martin, ...
Sos, Martin, Koker, Mirjam, Weir, Barbara, Heynck, Stefanie, Rabinovsky, Rosalia, Zander, Thomas, ...
Sos, Martin L., Koker, Mirjam, Weir, Barbara A., Heynck, Stefanie, Rabinovsky, Rosalia, Zander, Thomas, ...
Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions. (2009)
Sos, Martin L., Michel, Kathrin, Zander, Thomas, Weiss, Jonathan, Frommolt, Peter, Peifer, Martin, ...
Somatic genetic alterations in cancers have been linked with response to targeted therapeutics by creation of specific dependency on activated oncogenic signaling pathways. However, no tools...
Sos, Martin L., Koker, Mirjam, Weir, Barbara A., Heynck, Stefanie, Rabinovsky, Rosalia, Zander, Thomas, ...
Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1 (2009)
Barbie, David A., Tamayo, Pablo, Boehm, Jesse S., Kim, So Young, Moody, Susan E., Dunn, Ian F., ...
Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1 (2009)
Barbie, David A., Tamayo, Pablo, Boehm, Jesse S., Kim, So Young, Moody, Susan E., Dunn, Ian F., ...
Somatic mutations affect key pathways in lung adenocarcinoma (2008)
Ding, Li, Getz, Gad, Wheeler, David A., Mardis, Elaine R., McLellan, Michael D., Cibulskis, Kristian, ...
Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well- classified primary tumours. Here we report the results of a collaborative...
Genomic Approaches to Lung Cancer (2008)
Roman K. Thomas, Matthew Meyerson
Abstract The last decade has seen remarkable success in clinical targeting of activated oncogenes in cancer.We have applied gene expression profiling, high-density single-nucleotide polymorphism...
Major copy proportion analysis of tumor samples using SNP arrays (2008)
Li, Cheng, Beroukhim, Rameen, Weir, Barbara A, Winckler, Wendy, Garraway, Levi A, Sellers, William R, ...
Abstract Background Single nucleotide polymorphisms (SNPs) are the most common genetic variations in the human genome and are useful as genomic markers. Oligonucleotide SNP microarrays have been...
Takeshi Shimamura, Stefano Monti, Ulrich Steidl, Christopher J. Hetherington, Todd Golub, Matthew Meyerson, ...
Activating mutations in the epidermal growth factor receptor (EGFR) tyrosine kinase domain determine responsiveness to EGFR tyrosine kinase inhibitors in patients with advanced non–small cell lung...
Modeling genomic diversity and tumor dependency in malignant melanoma (2008)
Lin, William M., Baker, Alissa C., Beroukhim, Rameen, Winckler, Wendy, Feng, Whei, Marmion, Jennifer M., ...
Somatic mutations affect key pathways in lung adenocarcinoma (2008)
Ding, Li, Getz, Gad, Wheeler, David A., Mardis, Elaine R., McLellan, Michael D., Cibulskis, Kristian, ...
EML4-ALK fusion gene and efficacy of an ALK kinase inhibitor in lung cancer (2008)
Koivunen, Jussi P., Mermel, Craig, Zejnullahu, Kreshnik, Murphy, Carly, Lifshits, Eugene, Holmes, Alison J., ...
Shimamura, Takeshi, Li, Danan, Ji, Hongbin, Haringsma, Henry J., Liniker, Elizabeth, Borgman, Christa L., ...
Schlisio, Susanne, Kenchappa, Rajappa S., Vredeveld, Liesbeth C.W., George, Rani E., Stewart, Rodney, Greulich, Heidi, ...
VHL, NF-1, c-Ret, and Succinate Dehydrogenase Subunits B and D act on a developmental apoptotic pathway that is activated when nerve growth factor (NGF) becomes limiting for neuronal progenitor cells...
Cheng Li, Rameen Beroukhim, Barbara A Weir, Wendy Winckler, Levi A Garraway, William R Sellers, ...
© 2008 Li et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Characterizing the cancer genome in lung adenocarcinoma (2007)
Weir, Barbara A., Woo, Michele S., Getz, Gad, Perner, Sven, Ding, Li, Beroukhim, Rameen, ...
Somatic alterations in cellular DNA underlie almost all human cancers(1). The prospect of targeted therapies(2) and the development of high-resolution, genome-wide approaches(3-8) are now spurring...
Kaneko, Syuzo, Rozenblatt-Rosen, Orit, Meyerson, Matthew, Manley, James L.
Termination of RNA polymerase II transcription frequently requires a poly(A) signal and cleavage/polyadenylation factors. Recent work has shown that degradation of the downstream cleaved RNA by the...
Corrigendum: High-throughput oncogene mutation profiling in human cancer. (2007)
Thomas, Roman K, Baker, Alissa C, Debiasi, Ralph M, Winckler, Wendy, Laframboise, Thomas, Lin, William M, ...
Systematic efforts are underway to decipher the genetic changes associated with tumor initiation and progression1, 2. However, widespread clinical application of this information is hampered by an...
High-throughput oncogene mutation profiling in human cancer (2007)
Thomas, Roman K., Baker, Alissa C., Debiasi, Ralph M., Winckler, Wendy, Laframboise, Thomas, Lin, William M., ...
Characterizing the cancer genome in lung adenocarcinoma (2007)
Weir, Barbara A., Woo, Michele S., Getz, Gad, Perner, Sven, Ding, Li, Beroukhim, Rameen, ...
Lee, Jeffrey C, Vivanco, Igor, Beroukhim, Rameen, Huang, Julie H Y, Feng, Whei L, Debiasi, Ralph M, ...
BACKGROUND: Protein tyrosine kinases are important regulators of cellular homeostasis with tightly controlled catalytic activity. Mutations in kinase-encoding genes can relieve the autoinhibitory...
Lee, Jeffrey C, Vivanco, Igor, Beroukhim, Rameen, Huang, Julie H Y, Feng, Whei L, Debiasi, Ralph M, ...
Background Protein tyrosine kinases are important regulators of cellular homeostasis with tightly controlled catalytic activity. Mutations in kinase-encoding genes can relieve the autoinhibitory...
Jeffrey C. Lee, Igor Vivanco, Rameen Beroukhim, Whei L. Feng, Ralph M. DeBiasi, ...
BackgroundProtein tyrosine kinases are important regulators of cellular homeostasis with tightly controlled catalytic activity. Mutations in kinase-encoding genes can relieve the autoinhibitory...
Rameen Beroukhim, Ming Lin, Yuhyun Park, Ke Hao, Xiaojun Zhao, Levi A. Garraway, ...
Loss of heterozygosity (LOH) of chromosomal regions bearing tumor suppressors is a key event in the evolution of epithelial and mesenchymal tumors. Identification of these regions usually relies on...
Shimamura, Takeshi, Ji, Hongbin, Minami, Yuko, Thomas, Roman K., Lowell, April M., Shah, Kinjal, ...
Thomas, Roman K., Nickerson, Elizabeth, Simons, Jan F., Jänne, Pasi A., Tengs, Torstein, Yuza, Yuki, ...
Oncogenic Transformation by Inhibitor-Sensitive and -Resistant EGFR Mutants (2005)
Heidi Greulich, Tzu-Hsiu Chen, Whei Feng, Pasi A. Jänne, James V. Alvarez, Mauro Zappaterra, ...
Different EGFR mutations are associated with lung cancer. All of the classes can transform fibroblasts and lung epithelial cells, most are sensitive to erlotinib and gefininib, but exon 20 mutations...
Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis (2005)
Thomas LaFramboise, Barbara A. Weir, Xiaojun Zhao, Rameen Beroukhim, Cheng Li, David Harrington, ...
Amplification, deletion, and loss of heterozygosity of genomic DNA are hallmarks of cancer. In recent years a variety of studies have emerged measuring total chromosomal copy number at increasingly...
Oncogenic Transformation by Inhibitor-Sensitive and -Resistant EGFR Mutants (2005)
Heidi Greulich, Tzu-Hsiu Chen, Whei Feng, Pasi A. Jänne, James V. Alvarez, Mauro Zappaterra, ...
Background Somatic mutations in the kinase domain of the epidermal growth factor receptor tyrosine kinase gene EGFR are common in lung adenocarcinoma. The presence of mutations correlates with tumor...
Wadleigh, Martha, Ebert, Benjamin L, Wernig, Gerlinde, Huntly, Brian J P, ...
Polycythemia vera (PV), essential thrombocythemia (ET), and myeloid metaplasia with myelofibrosis (MMM) are clonal disorders arising from hematopoietic progenitors. An internet-based protocol was...
Using Single Nucleotide Polymorphism Arrays (2004)
Xiaojun Zhao, Cheng Li, J. Guillermo Paez, Koei Chin, Pasi A. Jänne, Tzu-hsiu Chen, ...
Changes in DNA copy number contribute to cancer pathogenesis. We now show that high-density single nucleotide polymorphism (SNP) arrays can detect copy number alterations. By hybridizing genomic...
Paez, J. Guillermo, Lin, Ming, Beroukhim, Rameen, Lee, Jeffrey C., Zhao, Xiaojun, Richter, Daniel J., ...
Major efforts are underway to systematically define the somatic and germline genetic variations causally associated with disease. Genome‐wide genetic analysis of actual clinical samples is,...
Tengs, Torstein, LaFramboise, Thomas, Den, Robert B., Hayes, David N., Zhang, Jianhua, DebRoy, Saikat, ...
We have developed a method for genomic representation using Type IIB restriction endonucleases. Representation by concatenation of restriction digests, or RECORD, is an approach to sample the...
Zhigang C. Wang, Ming Lin, Lee-jen Wei, Cheng Li, Er Miron, Gabriella Lodeiro, ...
Gene expression array profiles identify subclasses of breast cancers with different clinical outcomes and different molecular features. The present study attempted to correlate genomic alterations...
The catalytic subunit of yeast telomerase
Counter, Christopher M., Meyerson, Matthew, Eaton, Elinor Ng, Weinberg, Robert A.
Telomerase is an RNA-directed DNA polymerase, composed of RNA and protein subunits, that replicates the telomere ends of linear eukaryotic chromosomes. Using a genetic strategy described here, we...
Bhattacharjee, Arindam, Richards, William G., Staunton, Jane, Li, Cheng, Monti, Stefano, Vasa, Priya, ...
We have generated a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, we analyzed mRNA expression levels...
Scacheri, Peter C., Rozenblatt-Rosen, Orit, Caplen, Natasha J., Wolfsberg, Tyra G., Umayam, Lowell, Lee, Jeffrey C., ...
RNA interference (RNAi) mediated by short interfering RNAs (siRNAs) is a widely used method to analyze gene function. To use RNAi knockdown accurately to infer gene function, it is essential to...
Paez, J. Guillermo, Lin, Ming, Beroukhim, Rameen, Lee, Jeffrey C., Zhao, Xiaojun, Richter, Daniel J., ...
Major efforts are underway to systematically define the somatic and germline genetic variations causally associated with disease. Genome-wide genetic analysis of actual clinical samples is, however,...
Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments
Tengs, Torstein, LaFramboise, Thomas, Den, Robert B., Hayes, David N., Zhang, Jianhua, DebRoy, Saikat, ...
We have developed a method for genomic representation using Type IIB restriction endonucleases. Representation by concatenation of restriction digests, or RECORD, is an approach to sample the...
The Parafibromin Tumor Suppressor Protein Is Part of a Human Paf1 Complex
Rozenblatt-Rosen, Orit, Hughes, Christina M., Nannepaga, Suraj J., Shanmugam, Kalai Selvi, Copeland, Terry D., Guszczynski, Tad, ...
Parafibromin, the product of the HRPT2 (hyperparathyroidism-jaw tumor syndrome 2) tumor suppressor gene, is the human homologue of yeast Cdc73, part of the yeast RNA polymerase II/Paf1 complex known...
Menin and MLL cooperatively regulate expression of cyclin-dependent kinase inhibitors
Milne, Thomas A., Hughes, Christina M., Lloyd, Ricardo, Yang, Zhaohai, Rozenblatt-Rosen, Orit, Dou, Yali, ...
Mutations in the MEN1 gene are associated with the multiple endocrine neoplasia syndrome type 1 (MEN1), which is characterized by parathyroid hyperplasia and tumors of the pituitary and pancreatic...
Oncogenic Transformation by Inhibitor-Sensitive and -Resistant EGFR Mutants
Greulich, Heidi, Chen, Tzu-Hsiu, Feng, Whei, Jänne, Pasi A, Alvarez, James V, Zappaterra, Mauro, ...
Different EGFR mutations are associated with lung cancer. All of the classes can transform fibroblasts and lung epithelial cells, most are sensitive to erlotinib and gefininib, but exon 20 mutations...
Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis
LaFramboise, Thomas, Weir, Barbara A, Zhao, Xiaojun, Beroukhim, Rameen, Li, Cheng, Harrington, David, ...
Amplification, deletion, and loss of heterozygosity of genomic DNA are hallmarks of cancer. In recent years a variety of studies have emerged measuring total chromosomal copy number at increasingly...
Karnik, Satyajit K., Hughes, Christina M., Gu, Xueying, Rozenblatt-Rosen, Orit, McLean, Graeme W., Xiong, Yue, ...
Menin, the product of the Men1 gene mutated in familial multiple endocrine neoplasia type 1 (MEN1), regulates transcription in differentiated cells. Menin associates with and modulates the histone...
Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays
Beroukhim, Rameen, Lin, Ming, Park, Yuhyun, Hao, Ke, Zhao, Xiaojun, Garraway, Levi A, ...
Loss of heterozygosity (LOH) of chromosomal regions bearing tumor suppressors is a key event in the evolution of epithelial and mesenchymal tumors. Identification of these regions usually relies on...
Ji, Hongbin, Zhao, Xiaojun, Yuza, Yuki, Shimamura, Takeshi, Li, Danan, Protopopov, Alexei, ...
The tyrosine kinase inhibitors gefitinib (Iressa) and erlotinib (Tarceva) have shown anti-tumor activity in the treatment of non-small cell lung cancer (NSCLC). Dramatic and durable responses have...
The catalytic subunit of yeast telomerase
Counter, Christopher M., Meyerson, Matthew, Eaton, Elinor Ng, Weinberg, Robert A.
Telomerase is an RNA-directed DNA polymerase, composed of RNA and protein subunits, that replicates the telomere ends of linear eukaryotic chromosomes. Using a genetic strategy described here, we...
Bhattacharjee, Arindam, Richards, William G., Staunton, Jane, Li, Cheng, Monti, Stefano, Vasa, Priya, ...
We have generated a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, we analyzed mRNA expression levels...
Scacheri, Peter C., Rozenblatt-Rosen, Orit, Caplen, Natasha J., Wolfsberg, Tyra G., Umayam, Lowell, Lee, Jeffrey C., ...
RNA interference (RNAi) mediated by short interfering RNAs (siRNAs) is a widely used method to analyze gene function. To use RNAi knockdown accurately to infer gene function, it is essential to...
Paez, J. Guillermo, Lin, Ming, Beroukhim, Rameen, Lee, Jeffrey C., Zhao, Xiaojun, Richter, Daniel J., ...
Major efforts are underway to systematically define the somatic and germline genetic variations causally associated with disease. Genome-wide genetic analysis of actual clinical samples is, however,...
Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments
Tengs, Torstein, LaFramboise, Thomas, Den, Robert B., Hayes, David N., Zhang, Jianhua, DebRoy, Saikat, ...
We have developed a method for genomic representation using Type IIB restriction endonucleases. Representation by concatenation of restriction digests, or RECORD, is an approach to sample the...
The Parafibromin Tumor Suppressor Protein Is Part of a Human Paf1 Complex
Rozenblatt-Rosen, Orit, Hughes, Christina M., Nannepaga, Suraj J., Shanmugam, Kalai Selvi, Copeland, Terry D., Guszczynski, Tad, ...
Parafibromin, the product of the HRPT2 (hyperparathyroidism-jaw tumor syndrome 2) tumor suppressor gene, is the human homologue of yeast Cdc73, part of the yeast RNA polymerase II/Paf1 complex known...
Menin and MLL cooperatively regulate expression of cyclin-dependent kinase inhibitors
Milne, Thomas A., Hughes, Christina M., Lloyd, Ricardo, Yang, Zhaohai, Rozenblatt-Rosen, Orit, Dou, Yali, ...
Mutations in the MEN1 gene are associated with the multiple endocrine neoplasia syndrome type 1 (MEN1), which is characterized by parathyroid hyperplasia and tumors of the pituitary and pancreatic...
Oncogenic Transformation by Inhibitor-Sensitive and -Resistant EGFR Mutants
Greulich, Heidi, Chen, Tzu-Hsiu, Feng, Whei, Jänne, Pasi A, Alvarez, James V, Zappaterra, Mauro, ...
Different EGFR mutations are associated with lung cancer. All of the classes can transform fibroblasts and lung epithelial cells, most are sensitive to erlotinib and gefininib, but exon 20 mutations...
Karnik, Satyajit K., Hughes, Christina M., Gu, Xueying, Rozenblatt-Rosen, Orit, McLean, Graeme W., Xiong, Yue, ...
Menin, the product of the Men1 gene mutated in familial multiple endocrine neoplasia type 1 (MEN1), regulates transcription in differentiated cells. Menin associates with and modulates the histone...
Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis
LaFramboise, Thomas, Weir, Barbara A, Zhao, Xiaojun, Beroukhim, Rameen, Li, Cheng, Harrington, David, ...
Amplification, deletion, and loss of heterozygosity of genomic DNA are hallmarks of cancer. In recent years a variety of studies have emerged measuring total chromosomal copy number at increasingly...
Ji, Hongbin, Zhao, Xiaojun, Yuza, Yuki, Shimamura, Takeshi, Li, Danan, Protopopov, Alexei, ...
The tyrosine kinase inhibitors gefitinib (Iressa) and erlotinib (Tarceva) have shown anti-tumor activity in the treatment of non-small cell lung cancer (NSCLC). Dramatic and durable responses have...
Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays
Beroukhim, Rameen, Lin, Ming, Park, Yuhyun, Hao, Ke, Zhao, Xiaojun, Garraway, Levi A, ...
Loss of heterozygosity (LOH) of chromosomal regions bearing tumor suppressors is a key event in the evolution of epithelial and mesenchymal tumors. Identification of these regions usually relies on...
Lee, Jeffrey C, Vivanco, Igor, Beroukhim, Rameen, Huang, Julie H. Y, Feng, Whei L, DeBiasi, Ralph M, ...
Ingo Mellinghoff and colleagues sequenced theEGFR gene in glioblastoma samples and cell lines and identified missense mutations in the extracellular domain that suggest a new mechanism for EGFR...
Genome-Wide Analysis of Neuroblastomas using High-Density Single Nucleotide Polymorphism Arrays
George, Rani E., Attiyeh, Edward F., Li, Shuli, Moreau, Lisa A., Neuberg, Donna, Li, Cheng, ...
Kaneko, Syuzo, Rozenblatt-Rosen, Orit, Meyerson, Matthew, Manley, James L.
Termination of RNA polymerase II transcription frequently requires a poly(A) signal and cleavage/polyadenylation factors. Recent work has shown that degradation of the downstream cleaved RNA by the...
High-throughput sequence analysis of the tyrosine kinome in acute myeloid leukemia
Loriaux, Marc M., Levine, Ross L., Tyner, Jeffrey W., Fröhling, Stefan, Scholl, Claudia, Stoffregen, Eric P., ...
To determine whether aberrantly activated tyrosine kinases other than FLT3 and c-KIT contribute to acute myeloid leukemia (AML) pathogenesis, we used high-throughput (HT) DNA sequence ana-lysis to...
Major copy proportion analysis of tumor samples using SNP arrays
Li, Cheng, Beroukhim, Rameen, Weir, Barbara A, Winckler, Wendy, Garraway, Levi A, Sellers, William R, ...
Beroukhim, Rameen, Getz, Gad, Nghiemphu, Leia, Barretina, Jordi, Hsueh, Teli, Linhart, David, ...
Comprehensive knowledge of the genomic alterations that underlie cancer is a critical foundation for diagnostics, prognostics, and targeted therapeutics. Systematic efforts to analyze cancer genomes...
Functional Copy-Number Alterations in Cancer
Taylor, Barry S., Barretina, Jordi, Socci, Nicholas D., DeCarolis, Penelope, Ladanyi, Marc, Meyerson, Matthew, ...
Understanding the molecular basis of cancer requires characterization of its genetic defects. DNA microarray technologies can provide detailed raw data about chromosomal aberrations in tumor samples....
The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP
Yun, Cai-Hong, Mengwasser, Kristen E., Toms, Angela V., Woo, Michele S., Greulich, Heidi, Wong, Kwok-Kin, ...
Lung cancers caused by activating mutations in the epidermal growth factor receptor (EGFR) are initially responsive to small molecule tyrosine kinase inhibitors (TKIs), but the efficacy of these...
Schlisio, Susanne, Kenchappa, Rajappa S., Vredeveld, Liesbeth C.W., George, Rani E., Stewart, Rodney, Greulich, Heidi, ...
VHL, NF-1, c-Ret, and Succinate Dehydrogenase Subunits B and D act on a developmental apoptotic pathway that is activated when nerve growth factor (NGF) becomes limiting for neuronal progenitor cells...
Drug-sensitive FGFR2 mutations in endometrial carcinoma
Dutt, Amit, Salvesen, Helga B., Chen, Tzu-Hsiu, Ramos, Alex H., Onofrio, Robert C., Hatton, Charlie, ...
Oncogenic activation of tyrosine kinases is a common mechanism of carcinogenesis and, given the druggable nature of these enzymes, an attractive target for anticancer therapy. Here, we show that...
Predicting drug susceptibility of non–small cell lung cancers based on genetic lesions
Sos, Martin L., Michel, Kathrin, Zander, Thomas, Weiss, Jonathan, Frommolt, Peter, Peifer, Martin, ...
Somatic genetic alterations in cancers have been linked with response to targeted therapeutics by creation of specific dependency on activated oncogenic signaling pathways. However, no tools...
The tumor suppressor Cdc73 functionally associates with CPSF and CstF 3′ mRNA processing factors
Rozenblatt-Rosen, Orit, Nagaike, Takashi, Francis, Joshua M., Kaneko, Syuzo, Glatt, Karen A., Hughes, Christina M., ...
The CDC73 tumor suppressor gene is mutationally inactivated in hereditary and sporadic parathyroid tumors. Its product, the Cdc73 protein, is a component of the RNA polymerase II and...
Highly parallel identification of essential genes in cancer cells
Luo, Biao, Cheung, Hiu Wing, Subramanian, Aravind, Sharifnia, Tanaz, Okamoto, Michael, Yang, Xiaoping, ...
More complete knowledge of the molecular mechanisms underlying cancer will improve prevention, diagnosis and treatment. Efforts such as The Cancer Genome Atlas are systematically characterizing the...
Perera, Samanthi A., Li, Danan, Shimamura, Takeshi, Raso, Maria G., Ji, Hongbin, Chen, Liang, ...
Mutations in the HER2 kinase domain have been identified in human clinical lung cancer specimens. Here we demonstrate that inducible expression of the most common HER2 mutant (HER2YVMA) in mouse lung...