Genetic Future

Update 30/11/10: 23andMe has extended their 80% discount until Christmas, without a need for a discount code.

Personal genomics company 23andMe has made some fairly major announcements this week: a brand new chip, a new product strategy (including a monthly subscription fee), and yet another discount push. What do these changes mean for existing and new customers?


The new chip

23andMe’s new v3 chip is a substantial improvement over the v2 chip that most current customers were run on (the v2 was introduced back in September 2008). Firstly, the v3 chip includes nearly double the number of markers across the genome, meaning that it is able to “tag” a larger fraction of common genetic variants (“tagging” means that a marker on the chip is sufficiently highly correlated with other markers that it can be used to make a reasonable guess about someone’s sequence at those other markers). Secondly, the chip now includes additional custom markers targeting specific variants that the company thinks will be of interest to its customers.
The technical details: the v3 chip is based on Illumina’s HumanOmniExpress platform, which includes 733,202 genome-wide markers. The company has also added around 200,000 custom markers to the chip (vs ~30,000 on the v2 chip). We don’t yet have full details on what those custom markers are, but there’s a summary of the improvements over the v2 chip in the press release:
  • Increased coverage of drug metabolizing enzymes and transporters (DMET) as well as other genes associated with response to various drugs. 
  • Increased coverage of gene markers associated with Cystic Fibrosis and other Mendelian diseases such as Tay-Sachs. 
  • Denser coverage of the Human Leukocyte Antigen region, which contains genes related to many autoimmune conditions.
Deeper coverage of the HLA is particularly welcome – variants in this region are very strongly associated with many different complex human diseases (including virtually every auto-immune disease), and the v2 chip was missing several crucial markers. 
The addition of more rare variants associated with Mendelian diseases like cystic fibrosis is entirely unsurprising, but the devil will be in the details: in the arena of carrier testing 23andMe is up against the extremely thorough and experimentally validated platform offered by pre-conception screening company Counsyl. It will be very interesting to see the degree to which 23andMe focuses on the carrier testing angle in their marketing of the v3.
More power for imputation
From the perspective of those of us simply interested in squeezing as much information as possible out of our genetic data, the v3 chip is a welcome arrival. The additional markers present on the chip will substantially improve the power of genotype imputation – that is, making a “best guess” of our sequence at markers not present on the chip using information from tagging variants.
The HumanOmniExpress platform has some decent power here: in European and East Asian populations, 60-70% of all of the SNPs with a frequency above 5% found in the 1000 Genomes pilot project are tagged by a marker on the chip (in this context, “tagged” means “has a correlation of 80% or greater”). In effect, that means that being analysed at the one million markers on this chip allows you to make a decent inference of your sequence at around another 4.5 million other positions in your genome.
At the recent American Society of Human Genetics meeting, 23andMe presenter David Hinds suggested that the medium-term future for 23andMe rested not in moving to sequencing, but rather on expanding the role of genotype imputation. The new chip will certainly help with that. However, it’s worth emphasising that imputation is not a replacement for sequencing: it is only accurate for markers that are reasonably common in the population, meaning that it will miss most of the rare genetic variants present in your genome.
However, improved imputation with the extra markers on the v3 chip will mean that 23andMe should be able to do a decent job of predicting customer genotypes at the positions we currently know the most about – those arising from genome-wide association studies of common, complex diseases. I expect that many customers will see changes to their disease risk profiles as a result of the move to the new chip.
Over at Genomes Unzipped, we’ve already been looking at various approaches to imputation from our 23andMe v2 data, and we’ll put a post together soon looking at how this will improve with content from the v3 chip.
The new product strategy
There are two interesting things that 23andMe has done with the new product line: firstly, it has reversed the transient division of its products into separate Health and Ancestry components; and it has introduced a subscription model in which customers pay $5/month for updates to their account as new research findings become available (previously, customers paid a flat purchase fee and were then entitled to free updates).
The recombining of the Health and Ancestry products into a single Complete package is an extremely interesting move. As Dan Vorhaus notes, the previous separation of the two product lines was plausibly interpreted as a way for the company to pre-empt the possibility of a regulatory crackdown by the FDA: if regulators hammered the company’s ability to offer health-relevant tests directly to consumers, 23andMe could easily switch to its Ancestry product to maintain a revenue stream.
In the currently uncertain regulatory environment, the decision to reverse this division is an unexpected one. It certainly appears that 23andMe – flush with cash following a successful $22M funding round – is somewhat more confident than I am about the regulatory future for health-relevant genetic tests; I hope that confidence turns out to be warranted.
Subscription fees: good for customers
The decision to add a subscription fee may prove unpopular with customers (and has already received a qualified thumbs down from blogger Dienekes, albeit for perfectly sensible reasons). However, a business model based on providing continuous product updates that customers don’t pay for has never really looked like a viable long-term business model.
I personally see a subscription model as a positive move: it provides a steadier revenue stream for personal genomics companies, which means less focus on splashy discount drives. It also provides more of a financial incentive for the company to improve the ongoing experience of customers: under the current deal customers are locked in for the first 12 months, but after that 23andMe will need to convince them that it’s worth continuing to pay for additional content and features.
Other personal genomics companies (e.g. Navigenics) have long relied on some form of a subscription model, but typically at a higher cost. I think 23andMe is hitting a pretty reasonable price point here: I suspect $60/year would be seen by most customers as a fair price.
OMG discount!
That doesn’t mean that 23andMe has abandoned the discount drive approach just yet, of course: they’re currently offering v3 kits for just $99 (vs the retail price of $499), which must be purchased along with the previously mentioned 12-month subscription fee of $60. Non-US customers can also expect a ~$70 postage fee, based on comments on Twitter.
Anyone who missed out on the DNA Day sale and is keen to take advantage of the v3 content would be well-advised to get in quickly. The discount code is B84YAG.

Comments

  1. #1 Keith Grimaldi
    November 24, 2010

    Hi Daniel – very quick post, sleeping OK at nights now??

    I agree with you on the subscription move, it’s the major change they have made and has to be the way for the future as genotyping becomes hopefully less expensive and more common. There will be a lot of “free” competition, for example why should I pay 23andMe when there is Promethease? Of course there are many good reasons to do so and 23amdMe will have to keep it that way, good for subscribers.

    Like most information there will probably be free and paid for information – if you play the markets a little maybe yahoo finance is all you need, but if you are serious you’ll pay subs to Bloomberg, Reuters etc.

    It will be interesting to see though how ambitious any future “free” providers become.

    Very good news also on the HLA – I look forward to seeing the results

  2. #2 Keith Grimaldi
    November 24, 2010

    Ah, just saw your last tweet, still sleep deprived – more kudos for the quick post then!

  3. #3 Brian
    November 24, 2010

    HHY6P4 should work too!

  4. #4 Anon
    November 24, 2010

    No one likes to pay more, but as a 23andMe customer, I agree with the $5/month fee for the reasons you stated.

    But I’m surprised to hear about all this from your blog, since I’ve gotten no notice of any of the from the company itself. Then again, I haven’t logged into my account for a while.

    Time to see what’s been happening over there!

  5. #5 Ben
    November 25, 2010

    70$ postage fee? Well, again no test for me this year..

  6. #6 Anonymous
    November 25, 2010

    Anyone know if the v3 test can determine presence of the Cohen Modal Haplotype?

  7. #7 Mike Spear
    December 3, 2010

    I haven’t has any notice from 23andMe either so it is indeed odd to see it everywhere else except our email or 23andMe message inbox.
    It is also worth noting that from the beginning my Navigenics/Medcan test came with a $99.00 Cdn annual view.

    Mike

  8. #8 Bonnie
    December 4, 2010

    Thanks for the good info on the v3 chip, the most detailed I’ve seen! I mentioned to Joanna Mountain at ASHG that I was very interested in getting more HLA information, and would be willing to pay a little more to get it; looks like either she listened, or more likely, I happened to get interested in something they already had underway. I certainly intend to purchase an upgrade. Note that it has barely been mentioned how current customers can do this.

    @Anonymous, no, it can’t, and anyway, to talk about “the” CMH is out of date. There are multiple Cohen lineages; please see for example, “Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood” by Hammer et al (open access to full text).

    23andMe will allow you to see whether you share significant amounts of your DNA with Jews (mostly Ashkenazi) who’ve tested there, and a few of them may happen to have gotten (i.e. from FTDNA) the STR tests that can distinguish the Cohen lineages.

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