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Joining Signature, CMDX and Others, Affy Sets Sights on $500M Cyto Testing Market

Combining an increasing ability to survey copy number variations on its high-density SNP-genotyping chips with an interest in expanding its position in the array-based molecular diagnostics market, Affymetrix this month entered the cytogenetic-testing market with the debut of its Cytogenetic Solution product.
According to Affy, Cytogenetic Solution combines the firm’s 1.8-million-feature SNP 6.0 Array with a new assay format and specially designed software that it claims will make it easier for users to move from copy number and loss-of-heterozygosity data to results. Its chips are officially intended for research use only, but a company official said recently that the Cytogenetic Solution is being targeted to users that offer laboratory-developed tests under the guidelines of the Clinical Laboratory Improvement Acts.
“Affymetrix’ cytogenetic products are intended for RUO purposes, [but] clinical labs such as LabCorp are able to use RUO products to develop their own laboratory-developed tests when they establish the necessary performance characteristics and meet regulatory requirements applicable to their laboratory and the diagnostic service they are offering,” wrote Francisco Cifuentes, senior product manager of molecular diagnostics, in an e-mail to BioArray News last week.
Affy first announced its partnership with LabCorp in January (see BAN 1/29/2008). LabCorp had originally used chips produced by Spectral Genomics, now owned by PerkinElmer, in the cytogenetics testing service it launched in 2005, but decided to switch to the Affy platform due to the wider genomic coverage of its chip, LabCorp said at the time.
Affy CFO John Batty said at two recent financial conferences that the company sees its relationship with LabCorp as a sign of things to come. Affy now joins companies like CombiMatrix Molecular Diagnostics and Signature Genomic Laboratories in offering an array-based product for cytogenetic analysis, though CMDX and Signature rely primarily on a service model where they perform the analysis in-house, while Affy is more interested in selling the platform instead.
Batty said at Cowen and Company’s Annual Healthcare Conference in Boston last week that Affy envisions the market for cytogenetic-based testing to quintuple over the next three years, with the newer array-based platforms acting as a disruptive technology that will eventually displace current technologies like karyotyping and fluorescence in situ hybridization.
“This is a total market opportunity that we have previously not served, accounting for more than $100 million in 2008 and growing to approximately $500 million over the next three years,” said Batty.
He estimated that the market is divided between testing for postnatal mental retardation, developmental diseases, and autism spectrum disorder, and testing for cancer or cancer recurrence in primarily hematological cancers.

“This is a total market opportunity that we have previously not served, accounting for more than $100 million in 2008 and growing to approximately $500 million over the next three years.”

“When we look at conventional cytogenetic methods that include karyotyping and FISH, we find that these are methods that don’t have the necessary resolution, and in some cases they can take two weeks” to get results, Batty said. “We have now come up with a solution that is more cost effective and that can be performed much more rapidly.”
At Lehman Brothers’ Annual Global Healthcare Conference in Miami last week, Batty said that the firm’s move into the cytogenetics testing market was a natural extension of the “growth in copy-number studies” that is “fueling differentiation of products” sold by Affy.
The firm’s most recent whole-genome genotyping array, the SNP 6.0, includes nearly 950,000 probes for detecting copy number variation, and the company is now building a new database of human genomic variation that it will translate into next-generation products — a scenario that will likely affect the kinds of tools it offers to partners performing cytogenetic testing.
In January, CEO and Chairman Stephen Fodor said that Affy has taken the “entire known human variation database, about 12.5 million variations,” and created a set of chips that it is using to interrogate an additional 1,100 samples in order to generate a larger database (see BAN 1/15/2008).
Fodor said at the time that the new database will be ready during the first half of this year and will be used as a “resource to design our next-generation products” that will be “able to look at up to 10 million assays per chip in the near future.”
Research Use Only?
The idea that Affy can channel its size — it currently employs more than 1,000 staffers — plus its reputation in the market and its increasingly higher density arrays into success in the cytogenetics testing market is a powerful one.
At the same time, the company will be pushing up against players like Signature, which for years has offered testing on its internally developed arrays, as well CMDX, which launched a cytogenetic testing service in 2006, and other labs and firms like Baylor College of Medicine, Empire Genomics, and BlueGnome that also have eyes for the cytogenetic testing market.
Affy will also be competing against another leading chip vendor, Agilent Technologies, which manufactures custom designed oligo arrays for use in Signature and Baylor’s testing services (see BAN 10/23/2007).
One encouraging sign for the company could be that it will not only be targeting the diagnostic market, but the research market as well. In fact, Signature has decided to place the Cytogenetic Solution in its labs for research purposes.
“We are using Affy chips for research,” Signature CEO Lisa Shaffer told BioArray News this week. “We have investigators that want to run the chips, but don't have the facilities, so we are doing the chips for their research and giving them the results,” she said. She added that Signature also may use Affy’s platform to “look for deletions or duplications in apparently balanced translocations” in patients that show symptoms of developmental delay or other genetic abnormalities. 
Brynn Levy, associate professor of clinical pathology and director of the Clinical Cytogenetics Laboratory at Columbia University, said in a statement that such research will in turn improve the quality of current array-based cytogenetic testing as well.
"We are entering the realm where imbalances from 'genome to gene' can be detected,” Levy said. “As we gather and catalog precise information regarding the gene content of deletions and duplications in conjunction with well-characterized clinical information, our ability to make accurate genotype-phenotype predictions will be greatly improved."

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