Not Everyone on 23andMe Will Get the Latest Gene Chip Updates

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If you were early to the 23andMe spit party, you’ve probably noticed that you haven’t gotten any new reports about your genes from the company in a while. Not like more recent customers, whose inboxes receive the results of such analyses on the regular—like one with more specific ancestry estimates, which came out last year, or this one, for risk of type 2 diabetes, which arrived in March.

You haven’t gotten them because 23andMe, like most other direct-to-consumer DNA companies, untangles your genetic secrets using a relatively inexpensive technology called genotyping. Instead of sequencing all 6.4 billion base pairs of DNA, it takes strategic snapshots at just a few hundred thousand locations across the genome, looking at the different, important, and changeable parts. But since scientists frequently discover new links between DNA and disease, genes and geographies, and base pairs and behaviors, 23andMe keeps changing the silicon wafer chips it uses to snag all those DNA snippets. The more recently you spat into the tube and bought your 23andMe test—it was a best seller on Prime Day—the more up-to-date your test actually is. Which means, as many 23andMe users are finding out, being an early adopter doesn’t always pay off.

23andMe doesn’t make these chips, also known as arrays—it buys them from a genetic hardware company called Illumina. Each spot on an Illumina chip registers a particular variant, a place where one person’s DNA is different from someone else’s. The more variants you want to measure, the more complex—and therefore expensive—the chip. Think of it like upgrading your laptop; it probably costs more, but it’s probably faster and does cooler stuff, too. “One reason there’s been this evolution in genotyping arrays is a drive to be more efficient in terms of how many variants you’re measuring,” says Sarah Nelson, a biostatistician at the University of Washington who studies genetic technologies.

Those increases in efficiency and complexity are great for science but not always for consumer-facing genetic companies. People inherit their genomes in chunks, not gene by gene, so chip designers have been able to find predictable relationships between variants that are all near each other on a given chromosome. Make a chip that captures information about specific variants sprinkled across different chromosomes, and you also get information about neighboring variants at no extra cost. This is called imputation.“That’s fine for research purposes,” Nelson says, “but you can’t really use imputation for variants in health reports. If you’re giving information back to an individual about a rare variant that raises their risk of disease, you would want to have it directly measured.”

That’s the federal government stance too. In late 2013, the Food and Drug Administration told 23andMe that it couldn’t offer health information anymore—at least not until the company made some changes, including ensuring that any reports about customers’ disease susceptibility relied on clinically validated variants. These are small genetic differences with good evidence for how they influence people’s health. The company had recently switched to a new chip, its fourth version, and couldn't run the additional FDA-requested validation studies on the older chips, which Illumina was no longer producing for 23andMe.

In April 2017, the company started selling new customers its FDA-approved health reports for things like Alzheimer’s, Parkinson’s, and breast cancer. But the new rules and the new chip meant customers who tested on earlier versions were out of luck. The older technology wasn’t acute enough to read those sections of their genomes, and the policy didn’t give the company enough latitude to do it anyway.

Hundreds of 23andMe customers tested on those earlier chips have pleaded with the company for some way to get access to its latest features, like the health reports and improved ancestry estimates. Many worried about whether their old data was accurate. And a public records request from WIRED revealed that some customers filed complaints alleging deceptive advertising with the Federal Trade Commission. For close to a year, the company has advised all these customers to wait. A forthcoming chip upgrade policy, 23andMe promised, would give them access to its full suite of services. The old customers’ old spit would get run on the new chips.

But all those people salivating over the idea of new genetic insights have been disappointed. In an email last month, 23andMe announced that users on chip versions one, two, or three would have to pony up more cash. Access to the company’s latest ancestry reports will cost $69; the ancestry-plus-health experience will run $125. This is, of course, in addition to whatever people paid the first time around, which ranged from $1,000 in 2007 to $99 by 2013. They will have to send in more spit and wait three to five weeks to be retested on the latest chip. But unlike just buying a brand-new kit (which would require setting up a new profile), the upgrade process allows customers to merge their older chip data with the new stuff.

“Customers who are on the V3 chip version and older have not been receiving 23andMe reports for some time. These customers have been asking us for a pathway to upgrade their 23andMe reports at a discounted cost, and this upgrade policy is in response to that,” a 23andMe spokesperson emailed in response to WIRED’s questions about the upgrade policy. He noted that upgrading should not impact the accuracy or validity of reports generated on older chip versions. “In rare cases,” he wrote, “results may change—we will address any questions customers have in these instances should they arise.”

Chip upgrades also have ramifications far beyond asking customers to cough up more cash. Every time a company like 23andMe changes arrays, it also has an impact on genetic genealogy databases, and increasingly on the law enforcement agencies using them to catch criminals. Websites like GEDmatch rely on being able to compare the same chunks of DNA between people uploading their results from different genetic testing companies to generate matches between relatives. The new chip used by 23andMe (and recently adopted by FamilyTreeDNa and MyHeritage) has very little overlap with older chip versions—around 160,000 of 630,000 variants—making that comparison trickier and more prone to error.

Imputation software can help with backward compatibility, says Debbie Kennett, a UK-based genetic genealogist. However, those algorithms are something of a black box. “It’s difficult to judge the extent of the impact,” she says. Third-party tools, and the people who use them, have to be aware that the cheap and abundant data produced by testing companies like 23andMe can change at any time.

Upgrade policy or not, retesting isn’t always possible—people die, usually without leaving behind some saliva on ice for their genealogy-curious relatives. Which means that even though 23andMe says it has no timeline for further chip upgrades, new discoveries will continue to make existing arrays obsolete. And with companies starting to offer whole genome sequencing for less than $1,000, the long-term value of genotyping might turn out to not be such a great deal. 23andMe declined to say how many of its more than 10 million customers are eligible to buy into the chip upgrade program or how many already have. But as DNA testing gets more popular and more affordable, the episode is a useful reminder that such tests are consumer products and, like phones and laptops, they’re constantly evolving. Your genetic code might not be changing, but what you know about it always will be.

Corrected 7-18-19 1:10pm ET to reflect that 23andMe had upgraded to its fourth version chip prior to the 2013 FDA warning letter.


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