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Affymetrix Sees 'Rejuvenation' of SNP 6.0 Array Sales As It Lays Ground for New Cyto Offering

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By Justin Petrone

More than two years after it first launched a cytogenetics research offering on its SNP 6.0 genotyping array platform, Affymetrix continues to see strong demand for the product, according to a company official.

Richard Shippy, director of product marketing for molecular cytogenetics for the Santa Clara, Calif.-based company, told BioArray News last week that growing interest from cytogeneticists in SNP content has led to a resurgence of sales of Affy's SNP 6.0 chip.

Now the company is preparing a third-generation cytogenetics offering that will expand upon the SNP content of the 6.0 and the copy number variation content of the firm's Whole-Genome 2.7M Array.

"We are continuing to improve our software functionality, assay ease of use, streamlining our workflow, reagents, and kitting," Shippy said of Affy's cytogenetics product development. "We are also actively engaged in taking feedback from the community now to expand our portfolio of products that leverage the best qualities of SNP 6.0 and our 2.7M array to take us further," he said.

Affy first launched its Cytogenetics Research Solution in March 2008, bundling its existing SNP 6.0 array and internally developed software to reach cytogeneticists who are increasingly adopting array technology to help diagnose genetic abnormalities (BAN 3/25/2008). Last year, it rolled out its Cytogenetics Whole-Genome 2.7M Array, a new reagents kit, and upgraded analysis software, the Chromosome Analysis Suite (BAN 5/19/2009).

Initially launched in 2007 for use in genome-wide association studies, the 1.8-million-marker SNP 6.0 contains more than 906,600 SNPs and more than 946,000 probes for the detection of copy number variants. The 2.7M chip, in comparison, provides 2.7 million markers across the genome to detect CNVs, as well as 400,000 SNPs.

Shippy said that Affy's ability to make available SNPs and CNVs in one assay allowed it to enter the market, which includes competitive products from Agilent Technologies, BlueGnome, Illumina, Oxford Gene Technology, Roche NimbleGen, and others.

Shippy said the firm saw a "large uptake" of SNP 6.0 when it launched because it approximately half of the 1.8 million probes are non-polymorphic for copy number while the remainder are genotype-able SNP probes.

However, despite the introduction of the 2.7M, which was designed specifically for the cytogenetics market, Shippy said that the company now sees sales of SNP 6.0 rebounding as SNPs become more interesting to cytogeneticists.

"The cytogenetics field has transformed dramatically within the last two years with regard to the importance of SNPs," said Shippy. "In less than two years we went from SNPs being of modest interest within the cytogenetics community to now being absolutely essential," he said. "This shift in interest within the cytogenetics market towards higher density SNPs has rejuvenated interest in our SNP 6.0 array since the density of genotype-able markers is much higher than on the 2.7M array."

Part of the reason for the increased demand of the 6.0 also has to do with how the arrays are being used. Unlike comparative genomic hybridization platforms, arrays that contain SNPs can be used to detect uniparental disomy or consanguinity. He said that this ability has spurred adoption in certain regions, like the Middle East, because of higher rates of consanguinity, in which parents are closely related.

"SNPs are being used for gene level autozygosity mapping, assessing parent-of-origin for copy number changes, estimating low levels of mosaicism for small copy number changes, defining breakpoints more accurately, assessing loss of heterozygosity, UPD, and regions identical by decent due to consanguinity," he said.

Revived adoption of the SNP 6.0 doesn't mean that the 2.7M has fallen out of popularity. Just as some labs are interested in the higher SNP content of the 6.0, Shippy said that in other regions, the 2.7M-based offering is just as popular, partially because of the larger number of CNVs on the chip and also because the assay is less complex compared to the SNP 6.0.

"Our 2.7M platform is popular in laboratories which are just getting started with array-based cytogenetics where ease of use is more important than having high density genotype-able SNPs," Shippy said. "We are in a favorable position since we have two array options which may be suitable depending upon the customer profile."

'Solid Foundation'

To date, Affy's cytogenetics arrays have been made available in a cartridge format that runs on its GCS 3000 platform. Over the past two years, though, Affy has rolled out a new array strip format for its products, as well as two corresponding fully automated instruments: the GeneTitan, which can assay 96 arrays at one time; and the GeneAtlas, launched earlier this year, which can process strips of four arrays at a time.

Shippy said that while the GeneTitan was explicitly designed to support larger-throughput studies, like GWAS, the GeneAtlas could in the future be positioned for adoption by cytogeneticists.

"Most cyto labs run about eight samples per day, up to 30 samples a week," said Shippy. "You can run 32 a week on the GeneAtlas," he said. "We are considering leveraging that platform, but there are other options. The table is open and we want to offer different options to customers."

One advantage that customers may see by sticking with the GCS 3000 is that several assays, including Roche's CYP450 AmpliChip for drug metabolism testing and Pathwork Diagnostics' Tissue of Origin Test for cancer diagnosis, have been cleared by the US Food and Drug Administration for clinical use on the platform.

Affymetrix also has a "solid foundation" from which to proceed in any discussions with FDA. The firm has previously acknowledged discussions with the FDA about the best regulatory route for its cytogenetics offering.

"We already have an FDA-approved, 510(k)-cleared instrument which includes our cartridge-based fluidics station, scanner, and [diagnostics] software," Shippy noted. He said the platform "can be utilized for developing future products for cytogenetics."

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