GENE EXP. AND GENOTYPING

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The mission of the Gene Expression and Genotyping Facility (GEGF) is to facilitate implementation of high throughput genetic technologies for the research conducted by members of the Case community. The GEGF serves as a technical and consulting resource for Cancer Center members, as well as other investigators who have laboratories at Case Western Reserve University, University Hospitals of Cleveland, the Cleveland Clinic Foundation, the VA Hospital, and MetroHealth Hospital in the areas of high throughput expression analysis and genotyping. It is the only facility of its capability in Cleveland. This facility utilizes Affymetrix and Applied Biosystems (ABI) technologies to provide global and quantitative (on user-identified genes) gene expression analysis services. A diverse array of Affymetrix and ABI technologies are available to address a spectrum of genotyping needs, including whole genome scans, custom designed fine-mapping studies involving 3,000-10,000 SNPs and interrogation of small numbers (<100) of specific SNPs in thousands of samples. The core operates in a full-service mode with staff providing initial consultation, executing the chemistry, carrying out the analysis, and offering data trimming and data interpretation services. To carry out these technologies, the GEGF has 14 computers, an Affymetrix Workstation dedicated to data generation, 3 fluidics stations, 2 hybridization ovens and a GC3000 scanner with autoloader. ABI equipment includes a 7,900 Sequence Detection System, with a barcode reader, robotics allowing the capability to process 5,000 sample wells per day, and the modules for processing Low Density Arrays, 96- and 384-well plates. The GEGF also has 5 GeneAMP ABI 9700 PCR machines, with 96- & 384-well block capability and an ABI 6100 Nucleic Acid Prep Station. For PCR-based assays, the GEGF established an amplicon-free room, containing 2 PCR hoods, dedicated pipettors, small microfuges and minithermocyclers. Additional equipment includes: 2 Matrix robotic liquid handling systems, the PlateMate 2x2 (X-Y stage movement) and the PlateMate Plus (allows rapid reconfiguration from 96- to 384-well format), dedicated centrifuges, an Agilent Bioanalyzer and a NanoDrop Spectrophotometer, which quantifies nucleic acids in 1-2 ul samples. Turn-around time for sample preparation and analysis is <10 days for average size projects and satisfactory timetables are established for large projects during initial consultations. Cancer Center members receive a 35% discount on all GEGF provided services. The core has steadily grown from its inception in 2000, when we had 22 users and a single full-time staff member to its current staff of 51/2 and 142 registered users. Approximately 60 investigators use the GEGF every year and 30-50% of these are first time users, documenting that the GEGF continues to enjoy a healthy level of growth and a robust level of sustained work with repeat users. Finally, the GEGF has provided services for members from 8 of the Cancer Center's programs, and has played a role in securing more than 33 grants awarded to Cancer Center members.