Gene Expression Analysis Becomes Possible on Archive Samples

A whole-transcriptome amplification system will be available for gene expression profiling of formalin-fixed, paraffin-embedded (FFPE) samples with genechip 3' expression arrays

Affymetrix Inc. (Santa Clara, CA, USA) and NuGEN Technologies Inc. (San Carlos, CA, USA), a privately held company that develops and commercializes nucleic acid amplification and labeling systems for small and difficult samples, have agreed to co-market a system that enables researchers to access FFPE tissue samples derived from years of clinical studies previously inaccessible by traditional RNA amplification methods. The NuGEN WT-OvationFFPE system provides scientists the opportunity to conduct global gene expression analysis on their vast archives of small and degraded FFPE samples, using standard Affymetrix GeneChip 3' expression arrays.

The industry-standard Affymetrix 3' gene expression arrays enable researchers to simultaneously monitor genome-wide expression profiles. This global view helps scientists understand biologic mechanisms of complex diseases and processes, and identify new drug targets in ways never before possible. Utilizing gene expression profiles as novel biomarkers for conditions such as cancer or lupus, scientists are able to more accurately classify disease, predict clinical progression, and determine the likelihood of treatment success.

NuGEN's sensitive WT-Ovation FFPE system requires 50 ng of total RNA from FFPE samples for consistent, linear amplification yielding several micrograms of complementary DNA (cDNA). The process takes just six hours, and when used with NuGEN's FL-Ovation cDNA Biotin Module V2 for fragmentation and labeling, allows hybridization to GeneChip microarrays the same day. This simple, automated process saves time, labor, and precious samples, while delivering robust, high-quality results from degraded samples that may otherwise be more difficult to utilize for global gene expression profiling with standard Affymetrix 3' protocols.

For researchers, clinicians and pharmaceutical companies with thousands of valuable tissue samples archived from lung, breast, prostate, and colon cancer studies, this is a tremendous breakthrough, said Sue Pandey, NuGEN vice president of commercial operations. Investigators have been waiting for a solution that would enable the use of these samples and the extensive prognostic and prospective clinical data associated with them to gain insight into the causes of disease and response to treatments.

The NuGEN WT-Ovation FFPE System has unlocked valuable, high-quality biological data in our large archive of samples, said Jonathan M. Lancaster, M.D., Ph.D., chief, division of gynecologic surgical oncology at the H. Moffitt Cancer Center and Research Institute, who participated in Beta trials of the WT-Ovation FFPE system. This is a significant advancement in our cancer exploration, as it enables us to study low-abundance transcripts in severely degraded RNA--something we've previously been unable to accomplish. We're impressed with the product's sensitivity and reproducibility in such a simple process. We hope that success with this system will enable us to rapidly translate FFPE-based genomic signatures into clinical tools that will help guide therapy for women with gynecologic cancer.

NuGEN Technologies is focused on the development and commercialization of sensitive, rapid, and cost-effective amplification and labeling systems for genomic research. The company's technologies enable the comprehensive analysis and discovery of biologic mechanisms, cellular responses, and disease pathologies. The Ovation amplification and labeling system, the company's first commercially available product line, has applied these technologies to enhancing the sensitivity, convenience, and accuracy of gene expression analysis.

Affymetrix GeneChip microarray technology is the industry-standard tool for analyzing complex genetic information. After inventing microarray technology in the late 1980s, Affymetrix scientists have been dedicated to developing innovative products that provide researchers with a more complete view of the genome. These products continue to accelerate genetic research and enable scientists to develop diagnostics and tailor treatments for individual patients by identifying and measuring the genetic information associated with complex diseases.


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