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Paradigm Genetics Diversifies Array Services, Adding Affymetrix Platform


Paradigm Genetics this week announced two agreements with Affymetrix that will provide the Research Triangle Park, NC-based company and long-time Agilent Technologies customer with a second platform on which to conduct its microarray-analysis services.

The company on Monday said it has entered into a services agreement with Affymetrix based on the GeneChip platform and also signed an access agreement to use the technology for its internal research programs.

Paradigm executives told BioArray News that the announcement does not signal a change in the firm’s relationship with Agilent.

“We have been a long-time associate of Agilent Technologies and we are actually extremely pleased with how that relationship has been over the years,” Pat Hurban, head of investigational genomics for Paradigm, said. “We continue to use their platform for internal research as well as our microarray services business. We don’t really see that changing. I wouldn’t describe this as shifting gears so much as broadening our offering in a way that makes us more responsive to our potential customers.”

Paradigm, a nearly 200-employee company established in 1997, in April (see BAN, 4/4/2003) introduced a microarray services business as a preferred provider of Agilent Technologies’ microarray technology under a co-marketing agreement between the two companies. The services business leveraged a large-scale microarray analysis system set up to execute a $23.8 million five-year contract, awarded in October, with the National Institute of Environmental Health Sciences to produce gene expression data for a national reference database on the effects of chemicals on biological systems.

Triangle of Services

Paradigm is one of three Research Triangle-area commercial microarray-services providers. It now will compete directly with RTP-based Expression Analysis, an Affymetrix-platform based services provider, and ArrayXpress, a startup company (see BAN, 4/18/2003) spinning out of North Carolina State University, which employs microarray analysis techniques developed by Len van Zyl, an assistant professor in the school’s forest biotech-nology group.

The announcement does resonate with a growing interest in the provision of commercial microarray data services, ranging from NimbleGen’s proprietary platform, to the startup efforts of Memphis, Tenn.-based Genome Explorations, one of a list of Affymetrix-based commercial service providers that includes Phase-1 Molecular Toxicology of Santa Fe, NM, as well as Bio Matrix Research, Kurabo Industries, Mitsubishi Chemical Safety Institute, and Takara Bio in Japan.

“Affymetrix is the market leader and this opens many more doors to us to be able to provide services around their platform,” said Phil Alfano, Paradigm’s chief financial officer. “For us to exclude ourselves from any marketplace doesn’t make a lot of sense. We think it is good business.”

Negotiations took “less time than a pharma deal,” Alfano said. “When this relationship and the term made sense, it was not a hard deal to close.”

The companies are not disclosing financial terms of the arrangement.

“Paradigm is a quality microarray services provider and it makes sense for research service companies to provide access to all the platforms their customers might like to use,” Mel Kronick, chief scientist for Agilent, said in an e-mail. “The only exclusive agreement we have with Paradigm is in the use of Agilent’s microarrays for their toxicology grant with the NIEHS, and we have always supported each other’s efforts. We believe that Paradigm’s customers will receive the highest quality results by choosing Agilent microarrays, but it is important that customers have that choice.”


With this announcement, Paradigm will occupy a rare space as a provider of services on the two leading microarray platforms, adding new expertise to the knowledge already gained from its experience with Agilent’s platform.

“Both platforms will get you to the right answer when they are deployed in a very good way, such as by the scientists in my group, and if they are used in the right way,” said Hurban. “We are in a great position to help [customers] gain biological understanding and forget about all the culture wars going on between the various providers.”

The company has already purchased and installed new Affymetrix equipment including the scanner and hybridization station, said Hurban.

With its own internal research efforts, the company will also select the platform that it feels best suited for the task.

“For certain kinds of large-scale database-building types of experiments, having the Affymetrix platform as a single channel platform really shines in a lot of ways,” Hurban said. “You don’t have the reference sample problem that is often mentioned with two-color platforms. On the other hand, for certain types of experiments where we are looking at discrete comparisons directly between two samples, or a series of different samples, I think the two-color platform is a bit better.”

However, platform choice may not always be linked to issues like that. It might be as simple as the fact that a customer already has data in one format, and that linking it to new data from the same platform might be the most efficient method, he added.

Concordance issues between the platforms, he said, might require a more “delicate and sophisticated answer, than it has [received] in the past,” he added. “It’s really important to be able to map sequences directly onto the transcripts you are looking at in order to do the analysis,” he said.

In terms of data quality, Hurban said microarrays present new information previously unavailable to researchers.

“In terms of quality issues, it’s important that people understand that microarrays are not, for instance, quantitative PCR,” he said. “With the microarray platform, you can gain detailed knowledge, not as accurate as you can get with Q-PCR, but nonetheless very informative. As the marketplace moves to pre-manufactured arrays, we are going to see higher quality control and more reliable data. The same kind of shift happened when DNA sequencing equipment moved from slab gels to capillary devices.”


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