through the Custom Array laboratory. This second laboratory also supports the import and development of new array technologies e.g., micro-RNA arrays, that are of particular relevance to the current proposal. The Custom Array laboratory has been in operation for 7 years, and has processed over 5,500 samples to date. Core B is investing continually in state-of-the-art instrumentation: recent enhancements include a new spotted array printer (Qarray2) and several new Affymetrix fluidics workstations and scanners (in total 8 fluidics workstations and 3 high-resolution scanners each with autosamplers). Together, these laboratories have produced and assisted in the analysis of over 27,000 microarray profiles, thereby contributing critically to the research of this Program and other laboratories across SJCRH. Core B also includes substantial bioinformatics and biostatistics expertise that will provide support and computational hardware to the Program. These resources that are crucial for the completion of array based experiments include eight Ph.D.-level bioinformaticists (one of which is dedicated to this P01, Dr. Chunxu Qu) and 12 other highly skilled technical staff. Drs. Pounds and Zhao, who are faculty members in Biostatistics, also bring unique and extensive expertise in microarray data analysis. The high performance computing facility associated with Core B includes a 420-cpu Linux cluster, 150 Tb storage capacity, and a wealth of bioinformatics applications including LaserGene, Affymetrix LIMS system, Spotfire DecisionSite, R, and many other applications suitable for sequence and gene expression analysis. We seek partial support for one bioinformaticist dedicated to this Program (Dr. Chunxu Qu).

Public Health Relevance

To provide molecular profiling and bioinformatics support for investigation of pediatric brain tumors PROJECT/

National Institute of Health (NIH)
National Cancer Institute (NCI)
Research Program Projects (P01)
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Special Emphasis Panel (ZCA1-GRB-S)
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St. Jude Children's Research Hospital
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Zhan, Hong; Aizawa, Kenichi; Sun, Junqing et al. (2016) Ataxia telangiectasia mutated in cardiac fibroblasts regulates doxorubicin-induced cardiotoxicity. Cardiovasc Res 110:85-95
Grigaravicius, P; Kaminska, E; Hübner, C A et al. (2016) Rint1 inactivation triggers genomic instability, ER stress and autophagy inhibition in the brain. Cell Death Differ 23:454-68
Qaddoumi, Ibrahim; Orisme, Wilda; Wen, Ji et al. (2016) Genetic alterations in uncommon low-grade neuroepithelial tumors: BRAF, FGFR1, and MYB mutations occur at high frequency and align with morphology. Acta Neuropathol 131:833-45
Sturm, Dominik; Orr, Brent A; Toprak, Umut H et al. (2016) New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs. Cell 164:1060-72
Baker, Suzanne J; Ellison, David W; Gutmann, David H (2016) Pediatric gliomas as neurodevelopmental disorders. Glia 64:879-95
Phoenix, Timothy N; Patmore, Deanna M; Boop, Scott et al. (2016) Medulloblastoma Genotype Dictates Blood Brain Barrier Phenotype. Cancer Cell 29:508-22
Zhai, Yali; Kuick, Rork; Tipton, Courtney et al. (2016) Arid1a inactivation in an Apc- and Pten-defective mouse ovarian cancer model enhances epithelial differentiation and prolongs survival. J Pathol 238:21-30
Zhu, Liqin; Finkelstein, David; Gao, Culian et al. (2016) Multi-organ Mapping of Cancer Risk. Cell 166:1132-1146.e7
Patel, Yogesh T; Jacus, Megan O; Davis, Abigail D et al. (2016) Simvastatin Hydroxy Acid Fails to Attain Sufficient Central Nervous System Tumor Exposure to Achieve a Cytotoxic Effect: Results of a Preclinical Cerebral Microdialysis Study. Drug Metab Dispos 44:591-4
Morfouace, Marie; Nimmervoll, Birgit; Boulos, Nidal et al. (2016) Preclinical studies of 5-fluoro-2'-deoxycytidine and tetrahydrouridine in pediatric brain tumors. J Neurooncol 126:225-34

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