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Affymetrix's eBio Business Moving FlowCytomix Assays to Luminex Platform, Planning New Product Combinations


Less than a year after Affymetrix bought eBioscience, the array vendor is finding ways to combine its background in microarray and branched-DNA genotyping and expression with eBio's flow cytometry reagents and multiplex immunoassay portfolios.

As an example of this ongoing integration process, eBioscience, now one of four business units under the Affy umbrella, is moving its menu of FlowCytomix multi-analyte, bead-based immunoassays to the Luminex xMAP platform, said Tony Ward, eBio's vice president of commercial affairs.

San Diego-based eBio's FlowCytomix assays enable the simultaneous quantitative detection of up to 20 different analytes from blood, serum, and tissue samples using a flow cytometer. But given the number of existing Affymetrix QuantiGene and Procarta assays that run on Luminex's platform — close to 5,500, according to another executive — the company's management decided that it would make sense to offer eBio's FlowCytomix assays on the Luminex platform.

Ward told BioArray News that Affymetrix has "unique access" to DNA, RNA, and protein-measuring technologies, and claimed that there is "no one else" in the market that can offer customers that combination of assays on the Luminex platform. While he said that the firm's FlowCytomix assays have been "well received," they weren't available for use on Luminex's large installed base.

Luminex sells a number of instruments that process its xMAP assays, including its Luminex 100/200 and MagPix systems. When Luminex reported its fourth-quarter and full-year earnings in February, it noted that it has shipped close to 10,000 systems that support its xMAP technology to date (BAN 2/5/2013).

According to Ward, the "first batch" of catalog ProcartaPlex kits for use on Luminex instruments will launch at the American Association for Cancer Research, to be held in Washington, DC, later this week, and will include pre-configured panels for screening cytokines, including Th1, Th2, and Th17 responses.

'The Biggest Menu'

While Affymetrix is perhaps best known for its microarray portfolio, the company gained a growing menu of Luminex-ready assays when it acquired Fremont, Calif.-based Panomics in 2008 (BAN 12/16/2008). These include its QuantiGene Plex assay for measuring target RNAs, its QuantiGene DNA Multiplex assay for measuring DNA copy number, and its Procarta TF Plex assays for profiling the DNA binding activity of transcription factors. The company also offers mix and match Procarta Immunoassays, advertising "more than 260 protein assays and thousands of gene expression assays."

"When you look at our current number of distinct assays, we have the largest Luminex menu of any company in the industry," claimed George Bers, co-head of Affymetrix expression business unit. Bers, who served as Panomics' executive vice president for commercial operations before the firm's acquisition, said that after eBioscience converts its FlowCytomix assays for use on Luminex instruments, Affy will offer "something like 5,500 Luminex assays" in total, a number it hopes will work to its advantage.

"Think of it in terms of diagnostics," Bers told BioArray News. "If one company offers a lab 20 assays and the other offers the same lab 5,000 assays, the likelihood is that the lab will choose the one with the larger portfolio to supply its needs," said Bers. "At the end of the day, the battle fought in the trenches is over who has the biggest menu."

Though Affymetrix and Luminex's technologies are referred to as arrays in the marketplace, Affymetrix chips are used to survey millions of SNPs and copy number variants in a sample, while Luminex's xMAP assays can test each sample for up to 500 analytes. Because of these differences, Affymetrix sees Luminex's installed base as a means to selling more kits, rather than as a direct competitor with its own technology platforms.

"We have a strong relationship with Luminex," said Bers, "and are developing along that path."

Affymetrix did acquire a Bay Area startup called True Materials for $25 million in 2008, with plans to commercialize True's digitally encoded microparticle technology for lower multiplex nucleic acid and protein analysis, a part of the market dominated by Luminex and other firms. However, Andy Last, Affymetrix's executive vice president and general manager of genetic analysis, told BioArray News that commercializing True Materials' technology is "not a focus for us right now," and that Affy is more focused on Luminex bead-based applications."


Affy paid $315 million to acquire eBioscience last year in part to diversify its revenue sources. By incorporating eBioscience's flow cytometry and immunoassay reagents businesses, eBioscience contributions are anticipated to represent about a quarter of its projected revenues, offsetting the anticipated decline of Affymetrix’s expression microarray business from nearly half to roughly a third of its revenues, as CFO Tim Barabe stated at the time of the acquisition.(12/6/2011).

CEO Frank Witney told investors during Affy's fourth quarter earnings call that Affymetrix expects eBioscience will contribute about 22 percent of Affy's revenues in 2013.

But while diversifying its business was one objective of Affymetrix's decision to buy eBioscience, company executives said that they are at work on a number of products that combine their technologies.

"I think the complementarity of the product lines is pretty intriguing," said Ward. He said that by becoming part of Affymetrix, eBioscience has the opportunity to be more focused on serving drug developers than it had been previously. Since the acquisition, Affymetrix and eBioscience have been looking for opportunities "along the drug discovery continuum," said Ward, adding that the challenge for the company's different teams is "integrating product and bringing applications along"

During the Q4 call, Witney discussed one product combination that is close to launch. He said that Affymetrix has launched an early-access program for a product called QuantiGene FlowRNA, a "solution for low-plex analysis of RNA expression in single cells by flow cytometry." At the time of the call, Witney said that Affy had "received very positive feedback from our beta site" and looked forward to "establishing this unique capability as an important research tool."

According to Bers, the new product marries QuantiGene ViewRNA, in situ hybridization assays that enable the localization and visualization of RNA in cells or tissues, with eBioscience's flow cytometry capabilities.

"With QuantiGene view, you design a probe to any transcript in the human genome, just like a RT-PCR probe, but the difference here is that you stain the tissue on the slide and the probe will hybridize to the gene in question in the cells, so you get location as well as quantitative information," said Bers.

He claimed that the "single biggest clinical application" of flow cytometry platforms is leukemia and lymphoma subtyping. "In that application you are interrogating individual cells by sticking antibodies on the surface of a cell and labeling it with a dye because you want to quantify that cell in blood sample," he said.

By combining the two technologies, users of QuantiGene FlowRNA will be able to interrogate cells in a flow cytometry environment by monitoring the RNA transcripts inside the cell, with the added benefit of phenotyping cells with antibodies.
"Now, you can take one of the most ubiquitous cell [measurement] platforms on the planet and turn it into a genomic molecular biology platform," said Last.

According to Bers, it's possible the firms will find additional opportunities to combine their technologies. "Panomics and eBioscience [products] work nicely together in the area of plexed assays looking at proteins and RNA and DNA," Bers said. "Affymetrix [is] very strong in drug discovery, and eBioscience [is] very strong in immunology, cell biology, and stem cell applications," he said. "If we can start positioning products into each other's areas of expertise, we'll have opportunities for pretty significant growth," Bers added. "The unifying theme is that we can sell both product portfolios to all of our customers."