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Compugen and Sigma-Genosys Sign Deal to Design and Market Oligonucleotide Libraries


Compugen and Sigma-Aldrich subsidiary Sigma-Genosys have inked a deal to jointly design, manufacture, and market oligonucleotide libraries.

These products, called OligoLibraries, will include whole or partial sets of the human, mouse, and rat genomes. Customers will be able to access some sequence and other information about the oligos using Compugen’s LabOnWeb portal.

“The first libraries will be designed to represent the human, mouse, and rat genes already known,” said Compugen CEO Eli Mintz. “Then next step is to create a much larger library that represents the whole [human] transcriptome and many splice variants, but we have got to start walking before we can run.”

Compugen will contribute its oligonucleotide design algorithms, which it has previously used in microarray partnerships with Motorola and Pfizer, to the partnership. Sigma-Genosys will use its patented Abacus oligonucleotide synthesis technique to manufacture the product.

While Sygma-Genosys will leverage its well-oiled sales and distribution channels to market the bulk of the libraries, both companies will have the right to do so, and both will share in product revenue. Compugen has granted Sigma-Genosys a non-exclusive license to incorporate the libraries into its future products.

The parties did not disclose further financial terms of the collaboration, but Mintz said in an interview with BioArray News that he thought sales of the library would contribute significantly to revenues in the coming year.

“We expect oligonucleotide libraries to be a growing market,” said Mintz. “We have seen quite a lot of interest from collaborators and initial customers.”

Compugen of Tel Aviv, Israel, and Sigma-Genosys of The Woodlands, Tex., have organized the libraries based on the GeneOntology Consortium classification and terminology system.

To design the libraries, Compugen has used its LEADS platform of proprietary algorithms, which it also employs in its microarray chip design services. This platform enables Compugen’s bioinformatics team to model different features of the genome such as chimeric sequences, intron contamination, and alternative splicing in order to provide a complete picture of the human transcriptome, the complete complement of encoded mRNA transcripts that are expressed from the genome.

Through using these algorithms, Compugen said it can select oligonucleotides that reflect all of the splice variants for a particular gene, or alternatively, a particular splice variant.

“If you just take the longest EST from a UniGene cluster the way that Affymetrix used to do it, then choose an oligo from that EST, you may be measuring just one variant, or three out of five, or two,” Mintz said. “You have to know what you’re trying to measure.”

Like other oligonucleotide designers, Compugen also uses its algorithms to minimize the chance that the oligonucleotide does not hybridize to genes other than the target probe.

“Oligo design is a crucial step in order to get clean experiments in chips if you are working with mammalian sequence,” Mintz said. “Otherwise it’s garbage in, garbage out.”

The companies plan to initially target their OligoLibraries to core facilities in government and academic research facilities, vying for some of the market share that Qiagen subsidiary Operon currently commands with its array-ready oligos. “We believe that if the result from these core facilities prove to be clean and scientifically useful, the commercial entities will start looking at this [product] seriously,” Mintz said.


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