10 million DTC dense marker genotypes by end of 2017?


Today I got an email from 23andMe that they’d hit the 2 million customer mark. Since they reached their goal of 1 million kits purchased the company seems to have taken its foot off the pedal of customer base growth to focus on other things (in particular, how to get phenotypic data from those who have been genotyped). In contrast Ancestry has been growing at a faster rate of late. After talking to Spencer Wells (who was there at the beginning of the birth of this sector) we estimated that the direct-to-consumer genotyping kit business is now north of 5 million individuals served. Probably closer to 6 or 7 million, depending on the numbers you assume for the various companies (I’m counting autosomal only).

This pretty awesome. Each of these firm’s genotype in the range of 100,000 to 1 million variant markers, or single nucleotide base pairs. 20 years ago this would have been an incredible achievement, but today we’re all excited about long-read sequencing from Oxford Nanopore. SNP-chips are almost ho-hum.

But though sequencing is the cutting edge, the final frontier and terminal technology of reading your DNA code, genotyping in humans will be around for a while because of cost. At ASHG last year a medical geneticist was claiming price points in bulk for high density SNP-chips are in the range of the low tens of dollars per unit. A good high coverage genome sequence is still many times more expensive (perhaps an order of magnitude ore more depending on who you believe). It also can impose more data processing costs than a SNP-chip in my experience.

Here’s a slide from Spencer:

I suspect genotyping will go S-shaped before 2025 after explosive growth in genotyping. Some people will opt-out. A minority of the population, but a substantial proportion. At the other extreme of the preference distribution you will have those who will start getting sequenced. Researchers will begin talk about genotyping platforms like they talk about microarrays (yes, I know at places like the Broad they already talk about genotyping like that, but we can’t all be like the Broad!).

Here’s an article from 2007 on 23andMe in Wired. They’re excited about paying $1,000 genotyping services…the cost now of the cheapest high quality (30x) whole genome sequences. Though 23andMe has a higher price point for its medical services, many of the companies are pushing their genotyping+ancestry below $100, a value it had stabilized at for a few years. Family Tree DNA has a father’s day sale for $69 right now. Ancestry looks to be $79. The Israel company MyHeritage is also pushing a $69 sale price (the CSO there is advertising that he’s hiring human geneticists, just so you know). It seems very likely that a $50 price point is within site in the next few years as SNP-chip costs become trivial and all the expenses are on the data storage/processing and visualization costs. I think psychologically for many people paying $50 is not cheap, but it is definitely not expensive. $100 feels expensive.

Ultimately I do wonder if I was a bit too optimistic that 50% of the US population will be sequenced at 30x by 2025. But the dynamic is quite likely to change rapidly because of a technological shift as the sector goes through a productivity uptick. We’re talking about exponential growth, which humans have weak intuition about….

Addendum: Go into the archives of Genomes Unzipped and reach the older posts. Those guys knew where we were heading…and we’re pretty much there.

10 thoughts on “10 million DTC dense marker genotypes by end of 2017?

  1. As soon as regular physicians start to recommend genome sequencing, and/or insurance covers the cost, it will immediately get up to 50%.

    Many people today are simply worried that it will lead to discrimination (new unknown pre-existing conditions) when paying for their health insurance, or getting a new job. So in their mind it isn’t $100, it is $100 + imaginary big penalties.

  2. I expect to gain nothing from getting myself sequenced. But, I’d do it immediately for science, if someone was able to assure me a tax deduction for the expense.

  3. I did 23andme as well as Seeq and was considering getting my exome done, I found a place that would do it for ~$400. I also signed up for the Personal Genome project 6-7 years ago, and have not had my sample sequenced yet. I doubt that it will ever be.

    23andme gave me a good data to play with. Their website kinda sucks; the only feature that is interesting is the social aspect of it. It’s cool to trace inheritance from my parents to their grandchildren, as well as I found some relatives on my father’s side that we didn’t know previously. I may be missing a lot, since I haven’t really kept up on what new correlations they discovered.

    Seeq seemed like a really cool idea, but I haven’t really done anything with the data. A labmate of mine did some QC on it, and yes it really is like 0.1X coverage. I was going to cross-reference with the 23andme data, but I probably won’t get around to it. Once I get stable income, I’ll pay for a genome with better coverage and analyze that data. I did receive an email from Seeq this morning, apparently they’re changing to a for-profit company.

  4. re: seeq, it is going private. so there should be changes. but yes, it is very low coverage. but it is effective for ancestry at least.

    what test you do depends on what you want. ancestry has big database, but no y/mt or health or traits. 23andme has health upgrade and traits. ftdna has smaller database, but has y/mt (better y/mt than 23andme in terms of granularity last i checked). all of them cost around the same except for 23andme health upgrade.

  5. Thanks Razib, I’d like to get ancestries but i’m now not more convinced of the interest to get y/mt so Ancestry should do the job

  6. Henry,

    Most (all?) of the companies will give you the raw data. So, even though 23andme doesn’t give that many health traits anymore, you can use third-party programs like Prometheus to get more information. There are some for ancestry as well.

    I’m not 100% certain, but I think you still get your raw data from 23andme if you just pay for the ancestry.

  7. Thank you Odoacer and Razib. Indeed I expect to get the raw data to analyze it with third-party programs. As I’m in France 23andme would be more expansive (199$ including transport fees for European customers) so I may choose Ancestry

  8. Odoacer, yes, you do. My wife sent her sample to 23andMe and got her ancestry results only very recently (as in literally a few weeks ago), and I have only just downloaded her raw data file and run it to derive a health report for her.

    She chose 23andMe just because my daughter and I had both previously used them (when they were offering the $99 deal), despite higher cost now.

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