About Us

The objective of the Genomics Facility Core (GFC) is to provide full service applications of cutting-edge genomics technology to members of the SWEHSC. The GFC offers cost-effective genomic analyses and ready access to local expertise. The expertise of the Core’s directors enables the GFC to provide genome-wide analysis of the epigenetic effects of environmental toxicants. In addition to full service microarray-based analyses of gene expression, epigenetics, and copy number, the GFC provides consultation for sample preparation, sample quality control, and real time RT-PCR services in support of investigator’s studies. The GFC has established dedicated data analysis support for investigators through the biostatistics arm of the Integrated Health Sciences Facility Core.

Microarray technology provides a powerful approach for high-throughput parallel analysis of the entire genome. The GFC has continually updated and expanded applications offered in order to provide cutting edge genomics analysis to SWEHSC investigators. New applications developed and offered as complete services include genomic analysis of epigenetic modifications, both histone acetylation/methylation and DNA methylation, and analysis of genetic variability through array-based CGH. These new microarray applications, along with integrating bioinformatics into the GFC, have allowed investigators to identify biomarkers and pathways related to environmental exposures important to populations in Arizona, Mexico, and other parts of the world.

Mission

Mission of the Genomics Technology (GFC) is to consolidate resources and expertise to provide microarray-based analyses in a complete service to SWEHSC members.

 To support the vision and themes of the SWEHSC, the Genomics Facility Core provides Center investigators:

  1. A complete microarray service including sample quality control, target preparation, hybridization, scanning, quantitation, independent confirmation of results, and data analysis.
  2. Consultation on experimental design, sample preparation, and experimental protocols, and data interpretation.
  3. Access to a broad spectrum of complementary microarray platforms for analysis of both RNA and DNA differences in biological samples.
  4. Testing and implementation of new microarray technology, platforms, and approaches to maintain access to cutting edge technology.

 

 

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Recommendations for Sample Preparation

The high costs of microarray printers, scanners, and custom equipment, and the large effort required to develop microarray techniques make it impractical for each investigator wanting to use microarray technology to develop it on their own. The GFC enables the SWEHSC to leverage its resources to provide researchers with complete microarray service at a cost well below commercially available products.  Complete service includes consultation, hybridization, scanning, quantitation, confirmation, data archiving, and data analysis services at low cost or for free. Consultation and data analysis are free and include meeting with the GFC directors to design and plan experiments, define objectives, and interpret data. The low cost and time investment for investigators encourages use of microarray technology, and this, in turn, stimulates new areas of investigation while enhancing existing projects.

 The evolution of microarray technology over the past five years has yielded higher throughput, greater coverage, improved reliability, lower cost, and a wide range of applications. The GFC has expanded its range of services and platforms to include DNA-based analyses including: aCGH, SNP analysis, custom re-sequencing, promoter tiling, ChIP on chip (especially for epigenetic modifications to the “histone code”), and DNA methylation. The GFC also offers expanded options for gene expression profiling including the Affymetrix Sense Target (ST) GeneChips, Agilent’s Bioarray and custom chip platform, and Nimblegen’s custom genechip platform. The GFC also offers complete sample quality control in the form of spectrophotometric analysis and quantitative RNA quality analysis using the Agilent Bioanalyzer. The GFC has implemented automated hybridization to reduce technical variation; and upgraded software and scanner capabilities (e.g. the Affymetrix 7G scanner upgrade) to handle increased microarray density.