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Affymetrix to Start Clinical Trials for CytoScan HD in March, Plans FDA Submission by Midyear


By Justin Petrone

Affymetrix will initiate clinical trials for its CytoScan HD cytogenetics array in March, and hopes to submit the assay to the US Food and Drug Administration for clearance by the middle of this year, according to its CEO.

Frank Witney discussed the firm's plans during the JP Morgan Healthcare Conference in San Francisco last week. A company spokesperson this week confirmed the firm's plans but declined to further discuss its dealings with the FDA.

The move comes at a time when other large array vendors are inching closer to submitting their own array-based cytogenetic tests for regulatory clearance.

Affy launched CytoScan HD last July. The offering consists of its CytoScan HD array, reagent kit, Chromosome Analysis Suite software, and GeneChip instrument system. The array includes more than 2.6 million copy number markers, of which 750,000 are genotypeable SNPs and 1.9 million are non-polymorphic probes. Affy has claimed that CytoScan HD provides the "broadest coverage" of SNPs for detecting human chromosomal aberrations associated with genes related to constitutional and cancer cytogenetics (BAN 7/26/2011).

The array competes against offerings sold by rivals that include Illumina, Roche NimbleGen, Agilent Technologies, Oxford Gene Technology, BlueGnome, and others. Since its launch, CytoScan HD has been adopted by Arup Laboratories and Laboratory Corporation of America, among other labs (BAN 8/23/2011).

At JP Morgan, Witney said that the company is "very bullish" about CytoScan HD and called it the "best product on the market for cytogenetic analysis, offering unprecedented coverage and resolution." The firm has said previously that the chip was designed to comply with American College of Medical Genetics guidelines and has marketed the offering for both constitutional and cancer cytogenetics (BAN 5/10/2011).

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. However, many customers drifted back to the 1.8-million-marker SNP 6.0 Array prior to the launch of CytoScan HD (BAN 7/6/2010).

Most array vendors sell cytogenetics products for research purposes, and all of the larger vendors have pledged to take their chips through the FDA. Timelines for achieving clearance, though, have remained unclear as the FDA has continued to consider the appropriate approach for evaluating these platforms.

Like Affy, Illumina has also been "working with the FDA on clearance of our platform as an aid in the diagnosis of developmental delays," an Illumina spokesperson told BioArray News in an e-mail. "Clinical trials have started and we are on track to file our 510(k)s in 2012," she said, but did not elaborate.

Illumina has been planning FDA clearance for its cytogenetics offering for at least two years. In January 2010, Greg Heath, Illumina's senior vice president and general manager of diagnostics, said that the company would submit a cytogenetics package to the FDA as part of its preliminary investigational device exemption, or pre-IDE, process.

Heath said at the time that Illumina's pre-IDE submission would allow the firm to "start the discussion with the FDA about intended use, structure of clinical trials, and get some guidance from them about how we are going to approach this" (BAN 1/26/2010).

Heath's announcement was followed by similar statements from Affy, Agilent, and Roche NimbleGen. In April 2010, Roche NimbleGen said that it planned to achieve compliance with Good Manufacturing Process standards for its microarrays, followed by subsequent submission for clearance of its cytogenetic array products to the FDA (BAN 4/13/2011).

This week, a NimbleGen spokesperson told BioArray News that the firm is "in discussions with the FDA regarding study protocols" for its submission and is "nearing completion of our GMP implementation."

Agilent also said in 2010 that planned to submit a cytogenetics package to the FDA. The firm, which manufactures chips for a number of other companies, including OGT, BlueGnome, and CombiMatrix, received ISO 13485 certification as part of its planned submission. ISO 13485 is a standard for quality management systems for the design and manufacture of medical devices set by the International Organization for Standardization (BAN 3/30/2010).

The firm did not respond to a request for an update on its discussions with the FDA in time for this publication.

Array vendors decided to seek FDA clearance for their cytogenetic array platforms after the agency indicated that it would require labs that offer array-based chromosomal analyses to use cleared tests in the future.

In October 2009, a representative for the FDA's Office of In Vitro Diagnostics, which oversees the regulation of medical devices, told BioArray News that the agency had been reviewing the use of the tests. She said that the laboratory-developed tests used in clinical cytogenetic labs have been offered so far under the "regulatory discretion" of the agency, but that OIVD is now "going through a process of review and discussion" that could result in increased regulation of the tests (BAN 10/13/2009).

The agency later determined that it would require manufacturers to submit their offerings for clearance. However, the terms of the submission process have remained unclear. Affy this week did not respond to questions about the submission process for its cytogenetics offering.

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

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