No longer simply a wax museum

SAN CARLOS, Calif.—Proving true to its charter as a company that develops and commercializes nucleic acid amplification and labeling systems for small and difficult samples, NuGEN Inc. recently announced it forged a co-marketing agreement with Affymetrix Inc. for a solution that promises to unlock untold thousands of formalin-fixed, paraffin-embedded (FFPE) tissue samples for gene expression analysis using standard Affymetrix GeneChip 3 expression arrays.

NuGEN's recently launched WT-Ovation FFPE System is based on the company's novel linear isothermal RNA amplification technology it calls Ribo-SPIA and requires only 50 nanograms of total RNA from FFPE samples for amplifications that will yield several micrograms of cDNA.

"We have known for some time, based on what our customers are saying that there is demand for a tool like this in the research market," says Elizabeth Hutt, CEO of NuGEN. "There have not been a lot of robust technologies out there that would allow you to successfully amplify degraded samples."

For Affymetrix, the decision to enter a co-marketing agreement with NuGEN for its new product fits the company's partnering strategy of marrying enabling technology to help drive sales of its GeneChip line.

"People have needed FFPE profiling with three-prime arrays for a long time," says Tarif Awad, Ph.D., senior manager of pharma/industrial collaborations at Affymetrix. "And they wanted a solution that works with standard arrays. Until now, there hasn't been a system out there that does that."

Both companies see significant opportunity in the oncology research and clinical markets for biomarker discovery and validation, which should allow scientists greatly expanded access to a treasure trove of tissue samples estimated to number in the hundreds of millions worldwide. Awad says that what particularly adds value to the samples in conjunction with the combined NuGEN/Affymetrix solution is the underlying data associated with them.

Sue Pandey, vice president of commercial operations with NuGEN agrees. "This is a tremendous breakthrough. 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."

But FFPE sample quality is by no means a consistent. While there are a variety of factors that contribute to sample degradation, the most common factor is the age of the sample. To address these variations, NuGEN conducted a range of in-house tests using its FFPE system in order to produce guidelines for users to aid them in sample qualification and provide guidelines for assessing sample quality and accurately predicting the performance range of various samples.

"The reality is with FFPE samples there will be different levels of quality," says Awad. "But NuGEN did the work to allow researchers to score what kind of performance they can expect and, by doing this, calibrate their experiments."

While many of the details of the co-marketing arrangement were still to be worked out at press time, Hutt was quick to point out that the deal is not a co-marketing arrangement in name only.

"We will be recommending Affymetrix and will do a series of webinars with key thought leaders in the market to openly talk about FFPE," she says. "We will also be doing some joint sales meetings with the people from Affymetrix.to promote the FFPE solution."

Awad sees education, at least early on, as a key to getting the program off the ground quickly. "It's a pretty technical product and it will be important for us to demonstrate to customers what the technology is and the soundness of the technology," he notes. "I think NuGEN is going to get a lot of attention from this and for Affymetrix, it allows us to extend the value of our technology into a sample space we haven't penetrated effectively."