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FDA's DTC Dragnet Targets Illumina, but Affy Not Named Despite Having DTC Customers


By Justin Petrone

As part of its recent investigation into direct-to-consumer genetic tests, the US Food and Drug Administration last week sent letters to DTC firms 23andMe, Decode Genetics, Knome, and Navigenics, as well as to Illumina, requesting information on why they believe their tests or platforms do not need to be cleared by the agency.

The agency contacted Illumina because 23andMe and Decode use its research-use-only Infinium HumanHap550 array in their direct-to-consumer genetic-testing service. But it did not contact Affy, whose GeneChip platform, and specifically its SNP 6.0 arrays, are used by at least one DTC genetic-testing vendor.

In the letters, all dated June 10, the FDA asserts that the gene-analysis systems the companies are using are medical devices and therefore need to be approved by the agency. The FDA, which cites section 201(h) of the Food, Drug, and Cosmetic Act, 21 USC 321(h), urges the firms to contact it to obtain information that would enable them to "legally market" their services.

Writing Illumina CEO Jay Flatley, the FDA acknowledged that the company "has received FDA clearance or approval for several of its devices," but that its Infinium HumanHap550 array "is not one of them."

The FDA also noted that despite the chip being labeled "For Research Use Only," Illumina "is knowingly providing [it] to 23andMe and Decode Genetics for clinical diagnostic use without FDA clearance or approval."

The letter then reminded Illumina that in July 2009 it informed the FDA that 23andMe and Decode both order Illumina arrays for use in their consumer genetics offering. "For example, the 23andMe Personal Genome Service uses both the Illumina Infinium HumanHap550 array and a custom array for its Personal Genome Service," the FDA wrote.

The agency instructed Illumina to take "prompt action" and respond to its letter, but did not say the company can no longer sell the array to the two DTC vendors.

Illumina is "studying the letter," according to a spokesperson.

DTC genetic-testing vendor Pathway Genomics also uses Illumina's platform in its services, though it was not named in the Illumina letter (BAN 2/23/2010). The FDA last month sent Pathway a letter â€" prior to the agency's broader action last week â€" demanding to know why the company believes its tests do not require FDA clearance.

Left out of the FDA's dragnet was Affymetrix, a curious omission given that the company's GeneChip platform is used by Navigenics and erstwhile consumer genetics company Counsyl, both of which have publicly stated that they use Affy's technology in their services.

But according to an FDA spokesperson, the agency did not contact Affymetrix because "[i]t is our understanding that Navigenics does not use the Affy chip."

A Navigenics spokesperson this week confirmed that it has used, and continues to use, Affy's SNP 6.0 array in its service. She told BioArray News this week that Navigenics has "validated a number of technology platforms, including both [Life Technologies'] TaqMan SNP-genotyping assays and Affymetrix's 6.0 array, and utilizes the most appropriate platform as needed."

Navigenics launched its consumer genetics service, called HealthCompass, in 2007. In March 2009 it acquired Affymetrix's Clinical Laboratory Improvement Acts-certified Clinical Services Laboratory, which it rechristened Navigenics Laboratory (BAN 3/17/2009).

The Navigenics spokesperson said the company continues to use the lab to "perform all of our genetic tests for the analysis services included in Navigenics Health Compass."

However, an Affy spokesperson this week denied that Navigenics' service uses the company's products. Affy was "involved with early research studies but is not the supplier of their test," the spokesperson said.

In its letter to Navigenics, the FDA did not mention the platform it uses in its service. Addressed to CEO Vance Vanier, the letter claimed that Navigenics has "never submitted information on the analytical or clinical validity of its tests to FDA for clearance or approval."

However, the company's website states its Health Compass program "provides personalized information on which medications are more likely to work best for you given your genetic makeup, including warfarin and clopidogrel," and that the data generated from the Navigenics Health Compass "provide patients with genetic predispositions for important health conditions and medication sensitivities."

As it did with Illumina, the FDA's letter to Navigenics urged the company to contact the agency to discuss how it can "legally market" its service for "other uses."

Technology Mix

To be sure, most DTC genomics firms do not use just one RUO chip. Instead, firms interviewed for this article said they tend to augment their services with multiple technologies. For instance, Navigenics supplemented Affy's chips with TaqMan assays, according to Navigenics' spokesperson.

Also, Kári Stefánsson, Decode's executive chairman, told BioArray News in February that the company has been using catalog Illumina arrays as the "backbone" in its service, and then adds onto that "genotyping of individual SNPs and individual variants." He said it is "not unlikely that we will switch over to a custom-made chip at one point" (BAN 2/23/2010).

23andMe told BioArray News at the time that its service uses the Illumina HumanHap550 BeadChip along with a custom array of about 30,000 SNPs, while Redwoods City, Calif.-based Counsyl, which until recently offered its tests directly to consumers, uses an Affymetrix array that it has customized to help it test mutations involved in rare inherited diseases.

And David Becker, chief scientific officer at Pathway, said the company has used a custom Illumina microarray to generate the genotypic information required for its genetic health and ancestry reports.
According to Becker, Pathway's other tools include standard and targeted DNA sequencing, quantitative PCR probes, mass spectrometry, and microarrays manufactured by vendors other than Illumina.

"We use multiple technologies to cross-validate our markers, and to develop specific test panels," he said.