Update on the chip supply rumour from the FDA

Two days ago I reported a rumour that the FDA might have convinced genotyping chip provider Illumina to stop providing its products to direct-to-consumer genetic testing companies - a move that would effectively prevent these companies from being able to operate.

The rumour seemed plausible at the time, based on two pieces of evidence. Firstly, a letter sent to Illumina by the FDA in June warned the company that the use of its chips by personal genomics companies appeared to violate FDA regulations:

Although Illumina, Inc. has received FDA clearance or approval for several of its devices, we note that the Illumina® Infinium HumanHap550 array is not one of them and is labeled "For Research Use Only". Yet Illumina is knowingly providing the HumanHap550 array to 23andMe and deCODE Genetics for clinical diagnostic use without FDA clearance or approval.

Secondly, in a GenomeWeb report on Tuesday the Illumina CEO Jay Flatley is said to have confirmed a recent meeting with the FDA "to discuss the regulatory framework for DTC genotyping", and to have indicated that the company intended to "fully comply with the FDA's guidance"; Flatley is also quoted noting that the revenue from providing chips to DTC companies is "immaterial". This suggests that if the FDA did lean on Illumina to discontinue its chip supply to DTC providers there would be little motivation for the company to resist.

So, the rumour was plausible, but is it true? Yesterday I received a written statement from 23andMe indicating that as far as they were concerned it was false - "23andMe has no reason to believe there will be an interruption in the supply of Illumina chips at this time". 
Today, Mary Carmichael also has an enlightening interview with Alberto Gutierrez and Elizabeth Mansfield from the FDA. Here is the relevant segment: 
[Updated 06/08/10 to show the full version of the interview.]

There were several reports I saw this morning indicating that the FDA has "requested" that Illumina stop selling chips to DTC genetic-test providers. Is that true in whole or in part?
EM: We have asked Illumina to work with us to bring their devices into compliance with our regulations. We have not specifically requested that they stop selling them to anybody.

So they can continue supplying 23andMe and deCODEme with chips right now?
EM: We're working with them on that...

Illumina obviously isn't the only chip maker out there. Why is it the only one that is getting these letters? Are the other ones going to be called in as well?
AG: You can bet that with the original set of letters in 2009, Illumina was not the only one to receive a letter.

I'm sorry, I'm not familiar with the 2009 letters. What were those?
AG: We sent letters to several companies with direct-to-consumer chip arrays to come in and discuss the issue.

And did those companies come in?
AG: Yes, and I think that's part of what you saw with the public meeting on June 30 on the array issue and why several companies want to figure out a way to [unintelligible] ...

[The chips are labeled "research use only."] The DTC providers, when they sell these tests, aren't [necessarily] doing research. Doesn't that imply that Illumina does have to stop selling the chips to them?
EM: If they continue to label them that way, yes, that would be something that we would most likely take a little further action on. At the moment, they're working with us and we will see what they can bring to us in a reasonable amount of time without completely blowing up their business or the market or anything ...

So I guess if it's not being used for research only it needs a different type of [label or] approval?
AG: That's correct...

Until that happens, though, is it correct that the Illumina chips will remain on the market for direct-to-consumer companies to buy?
AG: [Pause] I think Illumina needs to figure out how they're going to move forward.

Carmichael also received a later email clarification from the FDA:

When asked to respond, the FDA e-mailed me with, "We have not asked Illumina to stop, but if they continue to make these chips available, we could explore other regulatory action."

So we have an answer, of a sort: the FDA has not specifically asked Illumina to discontinue its supply of chips to DTC companies, and there's currently no evidence that Illumina has already decided to do so. However, the FDA's email clearly indicates that the threat of regulatory action is still dangling ominously over the supply chains of DTC providers.

What the FDA still hasn't provided publicly is an explicit indication of exactly what DTC companies and/or Illumina need to do to stave off that threat. Stay tuned.

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A few hours after the interview, the agency wrote in an email that it had "not asked Illumina to stop, but if they continue to make these chips available, [it] could explore other regulatory action."

Daniel, you do yourself a disservice, your scoop is completely intact. Re-read the quote above. This official FDA email to Daniel Vorhaus says that they threatened "other regulatory action" if Illumina "continue[s] to make these chips available".

Those words were carefully chosen and it's pretty cut & dry. The FDA is surprised that this was publicly aired because their usual strategy is invisible backroom abuse, so they're now clouding the language and walking it back a bit, but what they did is clear.

Consider the phrasing. Surely Illumina isn't going to risk having the FDA explore "other regulatory action". A warning letter alone can take hundreds of millions of dollars off a stock price and tarnish their name. And forget about it if the FDA decides to send in inspectors or hold up approvals of all the things Illumina has in the FDA pipeline.

Gutierrez didn't want to admit in so many words that they made this threat during the interview, but make no mistake they knew what they were doing.

Illumina was only in the DTC space because it was (emphasize WAS) a growth market for them. Doubt Jay Flatley wants to screw 23andMe, but the FDA has a gun to his head and he has a responsibility to his employees. Even though everyone knows that Gutierrez and Shuren have gone crazy, he can't let Illumina be killed for 23andMe's imagined sins.