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Affymetrix to Launch Next-Gen Cytogenetics Array in Q3, Plans FDA Submission


By Justin Petrone

Affymetrix will later this year debut a high-density platform for cytogenetics research that it hopes will make it the top array vendor in that growing market.

The company also aims to have the new chip, called the CytoScan HD, cleared by the US Food and Drug Administration for clinical use, according to officials.

Richard Shippy, director of strategic marketing for clinical applications for the Santa Clara, Calif.-based company, said last week that Affy expects CytoScan HD to "set performance standards" in the cytogenetics research market, and believes that the new chip will have the "broadest degree of coverage for constitutional and cancer applications."

Shippy said that the array is compliant with American College of Medical Genetics forthcoming recommendations on the use of arrays in cytogenetics research. He also confirmed that CytoScan HD is "the array that we are taking through FDA clearance as an [in vitro diagnostic] for postnatal cytogenetics." He discussed the new product at Deutsche Bank Securities Health Care Conference, held in Boston last week.

Affy first entered the cytogenetics research market in 2008 with its Cytogenetics Research Solution, based on its SNP 6.0 Array. The company subsequently launched a second version of the product based on its Whole-Genome 2.7M Arrays, which included more information on copy number variants, but saw many customers drift back to the 1.8-million-marker SNP 6.0 Array (BAN 7/6/2010). Shippy said last week that more than 100 Affy customers currently use the SNP 6.0 chip for cytogenetics research.

According to Shippy, CytoScan HD contains about 2.5 million markers.

Shippy said the new chip offers "100 percent coverage of cancer genes as well as X chromosome genes," because "25 percent of known syndromes are on the X chromosome." The array also offers "100 percent coverage of constitutional genes," he claimed.

"What we are able to do is provide coverage of not only clinically relevant genes today, but clinically relevant genes tomorrow, meaning every single gene in the genome is covered," said Shippy. 750,000 of the markers on CytoScan HD are SNPs, he said.

The SNP content in the CytoScan HD will enable researchers to detect uniparental disomy, loss-of-heterozygosity, and consanguinity, conditions that comparative genomic hybridization arrays have been incapable of detecting. Affy won't have this market to itself, though, as both Agilent Technologies and Roche NimbleGen have launched or plan to launch chips with SNP content (BAN 3/29/2011).

The new CytoScan HD entails a cartridge array, reagents, and the firm's Chromosome Analysis Suite software. It runs on the Gene Chip Scanner 3000 or the GCS 3000 DX2 instruments. Shippy noted during his talk that there are currently 200 DX2 instruments and 2,000 GCS 3000 instruments installed worldwide that could support the new product.

CytoScan HD has already been alpha tested by a number of Affy partners. Shippy said that geneticists at Laboratory Corporation of America in Irvine, Calif.; Mission Hospitals in Asheville, NC; the Seattle Cancer Care Alliance; and the University of Nijmegen in the Netherlands have all used the array.

Among these early-access customers, Shippy singled out LabCorp as a "large user of our SNP 6.0 technology" and said the reference lab is "eager to move to the CytoScan array." LabCorp has been using Affy's platform since 2007 (BAN 1/29/2008).

Hutton Kearney, cytogenetics director at Mission Hospitals, told BioArray News this week that her experience with the alpha version of the CytoScan HD has been "positive." She stressed, however, that her experience is "preliminary" and based on the alpha version of the array.

"Our preliminary experience with the CytoScan HD has been exceptionally positive," Kearney said. "The array is well designed for clinical cytogenetic applications, and we are very pleased with the quality of data and platform performance," she added. Kearney said that her lab has been using the SNP 6.0 for about four years.

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According to Shippy, Affy designed the new chip in accordance with draft ACMG guidelines, which are expected to be published this summer. He told BioArray News this week that Affy was in its "development lifecycle prior to alpha when the manuscript was disseminated among array manufacturers for review" and had an "opportunity to ensure the design and performance of our new array demonstrated against these new guidelines."

He said that CytoScan HD is currently undergoing beta testing ahead of its scheduled launch. "Our external alpha testing was our opportunity to gain perspective in the commercial development stage," Shippy said. "The beta is our commercial readiness test, which is currently underway. We’re sending out the entire validated package —applications, documentation — for a try-out and a final check before release."

'Overtaking Agilent'

Most array vendors are already selling cytogenetics products, and all of the larger vendors, including Affy, Agilent, Illumina, and Roche NimbleGen, have pledged to take their chips through the FDA. Timelines for achieving clearance though have remained unclear as the FDA continues to consider the appropriate approach for evaluating these platforms (BAN 7/6/2010).

During last week's conference, Affy Chief Financial Officer Tim Barabe estimated the total market for constitutional cytogenetics to be around $500 million, with arrays comprising about $120 million in 2010, with a 20 percent annual growth rate.

Barabe estimated that Agilent currently has a 60 percent share of the cyto array market, and said that Affy is the second most successful company, with a 20 percent share. Not only does Agilent sell directly to cytogenetics researchers, but other firms that do, such as Cambridge, UK-based BlueGnome and Oxford, UK-based Oxford Gene Technology, sell arrays manufactured by Agilent.

Still, Affy is betting that CytoScan HD will be attractive enough to make customers switch to its platform from Agilent's.

"We fully expect that this is product is the type of product that will lead us to overtake Agilent in this market," said Barabe. "We expect to make a lot of progress toward the back half of this year and next year," he said.

Gaining share in the cytogenetics market is a priority for Affy, which has been trying to diversify its traditional business of selling expression and genotyping arrays in the research market by offering more focused assays for validation and routine testing.

Barabe noted that sales in the validation and routine testing category, which includes cytogenetic-themed arrays, were 20 percent of Affy's total revenue in 2010, up from 17 percent in 2011. Last quarter, these products accounted for 22 percent of sales, and he predicted that validation and routine testing will be 45 percent of the company's revenue in three years.

"We are migrating away from the RNA and DNA business, the research business, to this downstream business," said Barabe.

CEO Kevin King said during the firm's first-quarter earnings call last week that sales of cytogenetics- and cancer-related products grew 20 percent year over year, though the firm experienced a 9-percent drop in genotyping-related sales. He noted that growth in areas like cytogenetics should minimize the firm's dependence on less predictable markets, like that for genome-wide association studies (BAN 5/3/2011).

King also said in the call that CytoScan HD "will be one of our most important growth drivers for the company in the second half of the year."

Have topics you'd like to see covered in BioArray News? Contact the editor at jpetrone [at] genomeweb [.] com.