To get the full value out of microarray data, you have to strip the noise out of it, take many experimental variables into account, and apply complex statistical analyses. That''s a challenge not being adequately met by instrument manufacturers or the developers of bioinformatics software, according to Corimbia executive Ali Zareh, and his company is aiming to fill the gap.
"We are in a unique niche," said Zarah. "Upstream from analysis packages, and downstream from the instrument."
Corimbia''s Probe Profiler software is designed to replace the standard algorithms used with Affymetrix GeneChip microarray systems. "High-throughput platforms have a lot of intricacies in experimental design, and we want to capture that as much as possible," Zareh said. "We''re taking advantage of historical data to get a better understanding of how the probes are behaving, and analyzing the signal in a much more reproducible way."
The company claims that its approach increases the signal-to-noise ratio by as much as a factor of five, and provides up to an eight-fold improvement in sensitivity at the lower detection range. Since many genes have low signal intensity, the software may detect up to six times as many genes. Statistical measures of data quality and reliability are provided along with the results.
Corimbia, headquartered in Berkeley, Calif., was founded in 2000. Its president, Jim Veitch, was formerly a vice president at Gene Logic, where he headed up development of the GeneExpress data warehouse product and associated analysis tools. Zareh, who serves as vice president of business development, also hails from Gene Logic. Executive vice president Dave Wolfinsohn was a co-founder of Real Time Solutions. The chief software architect, Lewis Stiller, developed protein-folding models at Los Alamos National Laboratory and helped write the program that defeated chess champion Gary Kasparov.
The company is just beginning to scale up its marketing efforts. Pilot projects are underway with one large pharmaceutical firm and three biotechnology companies. Current academic collaborators include the University of California at San Francisco. The company''s business model assumes that most of the packages sold will be customized for the needs of a particular laboratory, although "as-is" components will also be available, Zareh said. Pricing is still under discussion. Meanwhile, Corimbia is relying on initial investments from its founders and revenue from consulting contracts with three customers.
A patent is pending on the algorithm for Affymetrix signal analysis, and the company may file patents on some other algorithms as well. "But in some cases, patenting would be counterproductive because we''d have to reveal our methods. Those we''ll keep private," Zareh said.
While gene expression profiling is Corimbia''s first application, it won''t be the last, Zareh predicted. Besides additional analysis tools for the Probe Profiler product, experimental design and LIMS packages are also on the drawing board. "One of the areas in which we see a great need is process control. We intend to play a role in that arena as well," he said.