GENE EXPRESSION CORE

University Of Colorado Denver, Aurora CO

Investigators

Linked publications, trials & patents

Abstract

Objective: The Genomics Shared Resource provides state-of-the-art facilities, technical support and services for scalable, innovative analysis of genetic variation and function, putting University of Colorado Cancer Center (UCCC) members on the cutting edge of cancer research. Services and Technologies: We use Affymetrix and lllumina oligonucleotide arrays and quantitative DNA/RNA methodologies to investigate gene expression/regulation changes, genotyping, and copy number variation. The GSR incorporates several platforms, including Affymetrix (with GeneTitan), lllumina (with iScan and HiSeq 2000), Agilent, and Combimatrix, establishing a comprehensive genomics research capacity, including expression, exon, tiling, re-sequencing and SNP/CNV, as well as custom design array services through collaboration with combimatrix por agilent Selected genes are analyzed using a Beckman Coulter GenomeLab GeXP genetic analysis system and Applied Biosystems real time PCR technology. For microarray data analysis, we provide members access to Partek Genomics Suite; GeneSpring; and Ingenuity pathway system and frequently use online public resources, including R and Bioconductor. More complex genomics data analysis is available to members through the Biostatistics and Bioinformatics Shared Resource. Consultation and Training: The GSR provides consultation for designing and analyzing excellent, reliable genomics experiments and helps keep members up to date as technology advances. Utilization: The Genomics Shared Resource is one of the highest volume academic Affymetrix microarray facilities in the country, having performed over 16,000 microarrays, including test arrays, for nearly 350 investigators over 10 years. Data from the Shared resource has been incorporated into over 300 published manuscripts to date. Management and Finances: This resource is UCCC-managed. Currently, 9% of the operating budget comes from CCSG support and 52% from chargebacks to UCCC members who represent 86% of users in 2010. The GSR requests $169,541 of CCSG support for 11% of its operating budget Future directions for the Genomics Shared Resource include upgraded microarray technologies, developing capacity with the newly-acquired lllumina HiSeq 2000 sequencer, moving into third generation sequencing possibly through the Pacific Biosciences Single Molecule Real Time (SMRT) DNA sequencing technology, and using highthroughput genetic analysis in translational research.