Affiliation: Translational Genomics Research Institute
- The BioIntelligence Framework: a new computational platform for biomedical knowledge computingToni Farley
The Translational Genomics Research Institute TGen, Center for BioIntelligence, Phoenix, AZ 85004, USA
J Am Med Inform Assoc 20:128-33. 2013....
- Synthetic lethal RNAi screening identifies sensitizing targets for gemcitabine therapy in pancreatic cancerDavid O Azorsa
Pharmaceutical Genomics Division, The Translational Genomics Research Institute, Scottsdale, Arizona 85259, USA
J Transl Med 7:43. 2009..Combinations of gemcitabine with other chemotherapeutic drugs or biological agents have resulted in limited improvement...
- Array-based gene expression, CGH and tissue data defines a 12q24 gain in neuroblastic tumors with prognostic implicationMaija Wolf
Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
BMC Cancer 10:181. 2010..Here, we present a framework, which integrates DNA, RNA and tissue data to identify and prioritize genetic events that represent clinically relevant new therapeutic targets and prognostic biomarkers for neuroblastoma...
- RNAi microarray analysis in cultured mammalian cellsSpyro Mousses
Cancer Drug Development Laboratory, Translational Genomics Research Institute TGen, Gaithersburg, Maryland 20878, USA
Genome Res 13:2341-7. 2003..In summary, this RNAi microarray platform, together with ongoing efforts to develop large-scale human siRNA libraries, should facilitate genomic-scale cell-based analyses of gene function...
- Harnessing the power of RNA interference to advance anticancer drug developmentSpyro Mousses
Cancer Drug Development Laboratory, Translational Genomics Research Institute, Gaithersburg, Maryland 20878, USA
Mol Cancer Ther 2:217-8. 2003
- RNAi phenotype profiling of kinases identifies potential therapeutic targets in Ewing's sarcomaShilpi Arora
Pharmaceutical Genomic Division, Translational Genomics Research Institute, Scottsdale, AZ 85259, USA
Mol Cancer 9:218. 2010..As part of novel target discovery in Ewing's sarcoma, we applied RNAi mediated phenotypic profiling to identify kinase targets involved in growth and survival of Ewing's sarcoma cells...
- RNAi-based functional pharmacogenomicsSukru Tuzmen
Pharmaceutical Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
Methods Mol Biol 700:271-90. 2011..In this chapter, we focus on the application of RNAi, with particular focus on HT siRNA phenotype profiling, to support cellular pharmacogenomics...
- High-throughput RNAi screening identifies a role for TNK1 in growth and survival of pancreatic cancer cellsMeredith C Henderson
Clinical Translational Research Division, Translational Genomics Research Institute, Scottsdale, AZ 85259, USA
Mol Cancer Res 9:724-32. 2011..The application of functional genomics by using HT-RNAi screens has allowed us to identify TNK1 as a growth-associated kinase in pancreatic cancer cells...
- Integration of genomic technologies for accelerated cancer drug developmentMark Basik
Translational Genomics Research Institute, Gaithersburg, MD, USA
Biotechniques 35:580-2, 584, 586 passim. 2003..This review examines the use of new and emerging DNA, tissue, and live-cell transfection microarray technologies that can be used to discover, validate, and translate information resulting from the completion of the Human Genome Project...
- High-content siRNA screening of the kinome identifies kinases involved in Alzheimer's disease-related tau hyperphosphorylationDavid O Azorsa
Pharmaceutical Genomics Division, Translational Genomics Research Institute, Scottsdale, Arizona 85251, USA
BMC Genomics 11:25. 2010..Identifying the kinases involved in the pathologic phosphorylation of tau may provide targets at which to aim new AD-modifying treatments...
- Advancing a clinically relevant perspective of the clonal nature of cancerChristian Ruiz
Clinical Translational Research Division, Translational Genomics Research Institute, Scottsdale, AZ 85259, USA
Proc Natl Acad Sci U S A 108:12054-9. 2011..We propose that our high-definition analyses of the genomes of distinct clonal populations of cancer cells in patients in vivo can help guide diagnoses and tailor approaches to personalized treatment...
- Nonsense-mediated decay microarray analysis identifies mutations of EPHB2 in human prostate cancerPia Huusko
Translational Genomics Research Institute, Cancer Drug Development Laboratory, 20 Firstfield Road, Suite 110, Gaithersburg, Maryland 20878, USA
Nat Genet 36:979-83. 2004....
- Targeting loss-of-function mutations in tumor-suppressor genes as a strategy for development of cancer therapeutic agentsHong Wang
The Translational Genomics Research Institute, Translational Drug Development Division, Phoenix, AZ 85004, USA
Semin Oncol 33:513-20. 2006..In this review, we discuss the feasibility of targeting loss-of-function mutations in tumor-suppressor genes for the identification of cancer-specific therapeutic agents...
- High-throughput siRNA screening as a method of perturbation of biological systems and identification of targeted pathways coupled with compound screeningJeff Kiefer
Pharmaceutical Genomics Division, Translational Genomics Research Institute TGen, Phoenix, AZ, USA
Methods Mol Biol 563:275-87. 2009..Most importantly, pathway tools allow the interrogation of HT-RNAi data to identify and prioritize pathway-based biological information as a result of specific loss of gene function...
- Genome scale cytometry: High content analysis for high throughput RNAi phenotype profilingDavid M Evans
Cancer Drug Development Laboratory, Translational Genomics Research Institute, 20, Firstfield Rd, Gaithersburg, MD 20878, USA Electronic
Drug Discov Today Technol 2:141-7. 2005..This review examines the current status of research in combining these tools.: ..
- Pancreatic cancer--could it be that simple? A different context of vulnerabilityDaniel D Von Hoff
Translational Genomics Research Institute, Phoenix, AZ 85004, USA
Cancer Cell 16:7-8. 2009..Could this finding provide us with a new method to attack pancreatic cancer?..
- A transforming mutation in the pleckstrin homology domain of AKT1 in cancerJohn D Carpten
Division of Integrated Cancer Genomics, Translational Genomics Research Institute, 445 N Fifth Street, Phoenix, Arizona 85004, USA
Nature 448:439-44. 2007..Furthermore, the E17K substitution decreases the sensitivity to an allosteric kinase inhibitor, so this mutation may have important clinical utility for AKT drug development...
- NMD microarray analysis for rapid genome-wide screen of mutated genes in cancerMaija Wolf
Medical Biotechnology, VTT Technical Research Centre of Finland and University of Turku, FIN 20520 Turku, Finland
Cell Oncol 27:169-73. 2005....
- High-resolution analysis of gene copy number alterations in human prostate cancer using CGH on cDNA microarrays: impact of copy number on gene expressionMaija Wolf
Medical Biotechnology, VTT Technical Research Centre of Finland and University of Turku, Turku FIN 20520, Finland
Neoplasia 6:240-7. 2004....
- Validation of short interfering RNA knockdowns by quantitative real-time PCRSukru Tuzmen
Pharmaceutical Genomics Division, Translational Genomics Institute, Scottsdale, AZ, USA
Methods Mol Biol 353:177-203. 2007....
- Impact of DNA amplification on gene expression patterns in breast cancerElizabeth Hyman
Howard Hughes Medical Institute NIH Research Scholar, Bethesda, Maryland 20892, USA
Cancer Res 62:6240-5. 2002..These genes may provide insights to the clonal evolution and progression of breast cancer and highlight promising therapeutic targets...
- Functional evidence implicating S100P in prostate cancer progressionGargi D Basu
Pharmaceutical Genomics Division, The Translational Genomics Research Institute, Scottsdale, AZ 85259, USA
Int J Cancer 123:330-9. 2008..Hence, S100P could be considered a potential drug target or a chemosensitization target, and could also serve as a biomarker for aggressive, hormone-refractory and metastatic prostate cancer...
- New insights into testicular germ cell tumorigenesis from gene expression profilingRolf I Skotheim
Department of Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, N 0310 Oslo, Norway
Cancer Res 62:2359-64. 2002....
- Discovery of genetic profiles impacting response to chemotherapy: application to gemcitabineHamdi Jarjanazi
Fred A Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
Hum Mutat 29:461-7. 2008..The results obtained using this novel methodology can be used to better design the clinical trials for effective study of the chemotherapeutic agents and thus provide a basis for individualized chemotherapy...
- Intersex-like (IXL) is a cell survival regulator in pancreatic cancer with 19q13 amplificationRiina Kuuselo
Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland
Cancer Res 67:1943-9. 2007..These findings implicate IXL as a novel amplification target gene in pancreatic cancer and suggest that IXL is required for cancer cell survival in 19q13-amplified tumors...
- Identification of molecular markers for endometriosis in blood lymphocytes by using deoxyribonucleic acid microarraysIdhaliz Flores
Department of Microbiology, Ponce School of Medicine, Ponce, Puerto Rico
Fertil Steril 85:1676-83. 2006..To identify molecular biomarkers for endometriosis in peripheral blood lymphocytes by using DNA microarrays...
- EphB2 expression across 138 human tumor types in a tissue microarray: high levels of expression in gastrointestinal cancersAlessandro Lugli
Institute of Pathology, University Hospital and Institute of Clinical Pathology, Basel, Switzerland
Clin Cancer Res 11:6450-8. 2005..To comprehensively evaluate ephrin receptor B2 (EphB2) expression in normal and neoplastic tissues. EphB2 is a tyrosine kinase recently implicated in the deregulation of cell-to-cell communication in many tumors...
- Short interfering RNA (siRNA)-mediated RNA interference (RNAi) in human cellsNatasha J Caplen
Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
Ann N Y Acad Sci 1002:56-62. 2003....
- Topoisomerase-II alpha is upregulated in malignant peripheral nerve sheath tumors and associated with clinical outcomeRolf I Skotheim
Department of Genetics, Institute for Cancer Research, The Norwegian Radium Hospital and University of Oslo, Norway
J Clin Oncol 21:4586-91. 2003..To identify target genes of clinical significance for patients with malignant peripheral-nerve sheath tumor (MPNST), an aggressive cancer for which no consensus therapy exists...
- Gene expression changes following androgen receptor elimination in LNCaP prostate cancer cellsIris E Eder
Department of Urology, University of Innsbruck, Innsbruck, Austria
Mol Carcinog 37:181-91. 2003..Further investigations are warranted to clarify their role in the AR signaling pathway and their susceptibility as a target for the treatment of prostate cancer...
- Clinical validation of candidate genes associated with prostate cancer progression in the CWR22 model system using tissue microarraysSpyro Mousses
Cancer Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA
Cancer Res 62:1256-60. 2002..001). These results illustrate a strategy for rapid clinical validation at the mRNA and protein level of gene targets found to be differentially expressed in cDNA microarray experiments of model systems of cancer...
- Clinical and functional target validation using tissue and cell microarraysSpyro Mousses
Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 8000, USA
Curr Opin Chem Biol 6:97-101. 2002..New high-throughput techniques, such as tissue and cell microarrays, will facilitate clinical and functional analysis of molecular targets...