Genomics High-Throughput Facility

The Genomics High-Throughput Facility Shared Resource (GHTF) was established in 1999 as a Comprehensive Cancer Center Shared Resource Core Facility.

• GHTF, a technology platform shared resource of the CFCCC since 1999
• Services ~70 investigators per year, including 18 unique cancer center users
• Staff­ed by SRAs Seung-Ah Chung and Valentina Ciobanu, each with more than five years experience, managed by Melanie Oakes, Ph.D., directed by Professor Suzanne Sandmeyer, Ph.D.
• Offers A­ffymetrix microarray analysis and Illumina HiSeq 2000 next-generation DNA sequencing
• Manages client access to Nanostring RNA analysis and Ion Torrent PGM DNA sequencing technologies
• Collaborates with Institute for Genomics and Bioinformatics, directed by Professor Pierre Baldi, Ph.D., and start­ed by Christophe Magnan, Ph.D. to administer initial NGS pipeline for DNA-, RNA-, and ChIP-Seq
• Co-administers Bioinformatics Shared Resource since 2010, start­ed by Jenny Wu, Ph.D., directed by Professor Chad Garner, Ph.D.
• Bioinformatics o­ffers experimental design consultation and custom analysis support
• GHTF and Bioinformatics occupy 2000 square feet of custom-designed space in Robert R. Sprague Family Foundation Hall
• Introduces CFCCC members to emergent technologies

SERVICES PROVIDED

Affymetrix Microarray Services:

• Consultation on experimental design strategies and provision of protocols for nucleic acid sample preparation
• Quality control utilizing an Agilent Bioanalyzer 2100 and NanoDrop 1000 spectrophotometer for RNA expression samples
• Standardized sample processing and evaluation using validated protocols for A­ffymetrix GeneChip arrays
• Assistance with basic statistical analysis of expression microarray studies
• Recharge-based access to RNA & DNA microarray analysis software

Next Generation Sequencing Services:

• Consultation on experimental strategy & provision of protocols for sample isolation
• Illumina HiSeq 2000 and Ion Torrent PGM sequencing
• Library preparation services for DNA-seq, RNA-seq, and Chip-seq, bisulfite treated, multiplex and other standard sequencing libraries
• Quality assessment of library DNA and quantification using prior to library sequencing
• Transmission of Illumina HiSeq 2000 data via the campus 10 GB network to the Institute for Genomics and Bioinformatics computer cluster for processing of raw data into FASTQ ‑les, alignment at user’s direction to reference genome, and downloaded to clients via FTP. Where requested and reference genome and sequence coverage allow, SNPs, indels, indicated and splice junctions considered
• Additional analyses are available on a fee-for-service basis

Cancer Center Bioinformatics Shared Resource Services:

• Advice to CFCCC members on optimal study design for high-throughput studies
• Assistance with grant proposals that include HT genomics/genetics components
• Guidance with data processing and analysis
• Provision of data analysis software and computer resources
• Direct custom analysis

FURTHER INFORMATION

To view the Genomics High-Throughput Shared Resource flyer click here.

For more information about this resource or to request service, please visit the Genomic High-Throughput Facility home page.

Director: Suzanne Sandmeyer, Ph.D.
Phone: 949.824.7571

Facility Manager: Melanie Oakes, Ph.D.
Phone: 949.824.6023

Bioinformatics Core Director: Chad Garner, Ph.D.
Phone: 949-824-2036

Finance Manager: Jeffrey McClain
Phone: 949.824.4577