Sample swaps at 23andMe: a cautionary tale

Personal genomics company 23andMe has revealed that a lab mix-up resulted in as many as 96 customers receiving the wrong data. If you have a 23andMe account you can see the formal announcement of the problem here, and I've pasted the full text at the end of this post.

It appears that a single 96-well plate of customer DNA was affected by the mix-up. This resulted in incorrect results being sent to customers, with alarming consequences in some cases; one mother posted on the 23andMe community about her distress upon discovering that her son's results were incompatible with the rest of the family:> Still upset I checked family inheritance and noticed my daughter shared with me, and then I checked my son's. He was not a match for any of us. I checked his haplogroup's and they were different from ours. I started screaming. A month before my son was born two local hospitals had baby switches. I panicked and I checked over and over. My kid's were sitting at the computer because we all wanted to see the results. My son laughed but he looked upset. I called my sister in tears.

Although 23andMe's announcement of the problem is commendably open, and it appears that the problem has now been fully resolved for the customers involved, there are numerous complaints in the announcement's comments thread about the length of time it took for customers to get feedback on their puzzling data. In addition, there's concern about the company's failure to perform even basic error-checking (e.g. confirming that the sex determined from genetic data was consistent with that specified by customers), and its vagueness regarding the corrective measures it plans to take to prevent this from happening in the future.This isn't the first time that personal genomics companies have mishandled customer data. In August last year, New Scientist's Peter Aldhous revealed sporadic problems with his mitochondrial DNA profile in deCODEme (which later turned out to be the product of a software glitch), and deCODEme also fumbled the process of translating 23andMe data last December.Mistakes happen - as any lab tech can testify, these sorts of sample swaps happen with frightening regularity even in clinical diagnostics labs. However, if the industry is to survive the massive scrutiny currently being pointed in its direction following the Pathway/Walgreen's debacle it must avoid any appearance of being amateurish; this type of mistake adds even more fuel to the regulatory fire burning under the industry. 23andMe needs to move fast to make sure that serious safeguards are put in place to make sure this never happens again. In addition to increasing lab quality assurance (at 23andMe's testing facility, LabCorp) 23andMe should introduce basic sanity-checking procedures to look for obvious data swap problems.Customers also have a role to play here in checking their own data for obvious mistakes - and it is noteworthy that in this case the sample problems seem to have been detected by customers rather than the company. This is a good time to repeat my advice from last year:> However, this incident serves as a canary in the personal genomics coal-mine - a warning of the challenges that lie ahead for companies in ensuring that massive, complex genetic data-sets are presented accurately to consumers.

It's also a useful reminder to personal genomics consumers to not take their results for granted. The process between spitting into a cup and viewing your genetic results online involves multiple steps where things can go wrong, ranging from errors in sample tracking (the most pernicious and difficult to correct), through genotyping problems (usually much easier to spot), to errors in data analysis and display.

In general the odds of a given genetic data-point being wrong are very low, but they're sufficiently far above zero to warrant caution in making too much out of any single result - mind you, given the extremely small effect sizes of most of the variants currently assayed by personal genomics companies, that's good advice anyway. Certainly it would be a good idea for customers to seek independent validation of *any *result if they intend to use it to guide serious health or lifestyle decisions.

But the most important piece of advice for personal genomics customers is to engage with your data. Aldhous only detected these anomalies because he was exploring his own genetic data in multiple ways, cross-checking it against both other data and his own (informed) expectations, and was persistent enough to follow up on the strange results he found.

That's a good example for other personal genomics customers to follow: rather than being a passive recipient of genetic forecasts, dig into your data and see if it makes sense, and keep asking questions until it does. In addition to making it more likely that you'll pick up any errors in your results, you'll also develop a much deeper understanding both of the nature of genetics and of your own genome.

Some errors you won't be able to spot, but make sure you're informed enough to spot at least the most glaring problems.Here's the full announcement from 23andMe:

We recently determined that a number of new 23andMe customer samples were incorrectly processed by our contracted lab. We want to clarify what happened with the sample errors, how it happened and what we're doing to prevent it from happening again. Providing each and every one of our customers with accurate data is 23andMe's number one priority, and we fully realize the gravity of this incident. Up to 96 customers may have received and viewed data that was not their own. Upon learning of the mix-ups, we immediately identified all customers potentially affected, notified them of the problem and removed the data from their accounts. The lab is now concurrently conducting an investigation and re-processing the samples of the affected customers and their accurate results will be posted early next week. We expect the investigation will be complete over the next several days and we will provide further details when we have them.

We are currently putting additional procedures in place that will add an extra layer of safeguards to help assure that similar incidents do not occur in the future. We are deliberating on a process that would include removing manual steps at the lab, completely automating the sample analyses, and implementing further checks of the data before it gets loaded into customer accounts. Please be assured that our testing laboratory's processes comply with strict professional, regulatory, and corporate quality assurance standards for ensuring that all laboratory test results are accurate. The laboratory will adopt corrective action as warranted based on the findings of the investigation.

The science behind 23andMe's personal genetics service remains proven and sound. We recognize that this is a very serious issue and your trust is of the utmost importance. We hope that this helps clarify what has happened and what we are doing to prevent these problems in the future. Please contact me at khomenko@23andme.com if you have any further questions. We appreciate your comments and feedback.

Update 8/6/10: 23andMe has provided details of the cause of the incident and the steps it has taken to prevent similar problems in the future.