Mission: The objective of the CCCWFU Microarray Shared Resource is to provide Cancer Center members with a competitive and cutting-edge environment for cancer genomics research. The Shared Resource accomplishes this goal by providing faculty with comprehensive and cost-effective microarray technologies and bioinformatics support to facilitate RNA expression profiling, single nucleotide polymorphism (SNP) genotyping, genome copy-number analysis, and methylation profiling using Affymetrix GeneChip oligonucleotide arrays. The accomplishment of these objectives has, in part, been facilitated by recent modifications to the Shared Resource, including the recruitment of Dr. Lance D. Miller as Director, and the addition of a microarray bioinformatics expert to facilitate high quality, detailed analysis of microarray data. Assets: The Microarray Shared Resource has a modern infrastructure that includes the GeneChip Scanner 3000 7G multi-color scanner (recently upgraded to accommodate the MegAllele system for targeted genotyping);three GeneChip 450 fluidics stations;two GeneChip hybridization ovens and four high-speed computer workstations for data analysis workflows. Computational tools for data processing and low-level array analysis are provided by the Affymetrix GeneChip Command Console software (AGCC; released September 2008) which includes basic solutions for data normalization, analysis of expression, genotype and copy-number data, registration of samples and arrays, and management of multi-chip datasets. For advanced data analysis, the Shared Resource now maintains an annual license to the Partek Genomics Suite software - a comprehensive suite of advanced statistical methods and interactive data visualization tools. Usage &Future Directions: In the previous 1-year reporting period, the Microarray Shared Resource has been fully engaged, operating at near maximal capacity, performing 885 microarray hybridizations and providing technical and analytical resources to more than twice as many funded Center members as compared to previous years (1.8 to 5.5-fold more than seen in the past 3 years). Continued development of bioinformatics resources and acquisition of new array technologies are expected to further bolster cancer genomics research at the CCCWFU in the coming years.
Cancer is a disease of the genome and microarray technologies are a valuable resource for investigating the genomic and molecular underpinnings of cancer formation, progression and response to treatment. Further development of the bioinformatics capabilities of the Shared Resource will be valuable to the clinical translation of discoveries made by Cancer Center investigators.
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