The buzz leading up to this week's Consumer Genetics Show in Boston suggested that a major announcement would be made by the CEO of genomics technology provider Illumina, Jay Flatley. Illumina provides the most popular second-generation sequencing instrument currently on the market, the Genome Analyzer II, and has been making noises about moving into the personal genomics industry since at least the beginning of the year, so the announcement itself was not exactly a shock: Illumina is launching a personal genome sequencing service.
The service will consist of complete genome sequencing to a depth of 30X (meaning that each base in the genome is sequenced an average of 30 times), using Illumina's paired-end short-read technology. Coverage of 30X with short-read sequencing is reasonable; it will miss around 10% of the genome that is too repetitive to span with short reads, but in the remainder it will call most single-base variants with >99% accuracy, and will do a fairly good job of picking up small insertions and deletions and larger rearrangements (so-called structural variants).
The big surprise for me in this announcement is the price - or rather, the fact that the price isn't actually all that surprising. At $48,000, the cost represents a halving of the price of the current best commercial offering on the market ($99,000 fromÂ Knome), but it's still way out of the price range of most of us - and substantially above the $10-20,000 figure that FlatleyÂ discussed back in FebruaryÂ as the price its first customers would pay. This is incremental inching forward rather than a great leap towards the democratisation of genome sequencing.
Sequencing a whole genome with short-read technology is difficult, but the real challenge is the next bit: translating the assembled sequence into useful information. Illumina will not be doing the interpretation of genome sequences themselves, butÂ will instead draw on the expertise of relatively well-established personal genomics companiesÂ 23andMe, deCODEme, Navigenics and Knome. Customers will apparently have the option of choosing which of these providers they go through for their analysis, who can then add their own additional fees for this crucial stage.
As the field evolves, "it could be in the long-run that [physician involvement] is not a requirement," Flatley said. "We thought it's better for us to do it this way in the beginning, to take the highest road we could find."
"Ultimately , we think the data need
to be mobile connected and wind up in the cloud," said Flatley. "You
can't fit the entire genome onto an iPhone today, but once we've
calculated the Vnome (variant genome), this becomes feasible."
Flatley dazzled the audience by
showing a preliminary concept of the iPhone personal genomes app,
produced by a developer in a mere ten days. Following fingerprint
identification, the app would present data on many different diseases
and traits. It could list by disease, drug response, or chromosome;
search by genes, share facilities with friends and family, and so on.
Finally, Flatley joked that if people spend too much time analyzing
their genome on their iPhone and the boss walks in, "all they have to
do is shake and they'll be right back to the spreadsheet analyzing
their sales numbers."
"since most people will only need their genome sequenced once very cheap sequencing will rapidly result in a depletion of the sequence generation market."
Complete Genomics claims that there is life after one sequence per person: http://www.completegenomics.com/applications/default.aspx
Is this only human genomes, or could someone get a $5m grant, and pay them to sequence, for example, a hundred odd bird genomes?
Fascinating detailed description of Illumina's new genome launch. As always, I appreciate your well-thought out opinions and updates regarding the personal genomics market!
Daniel, great summary! I think calling a 50% price cut "subtle" is a bit harsh. Knome's move, no?
Post #2 raises an interesting issue: I didn't hear anything in Jay's talk to indicate this is ONLY for human sequencing (c.f. say Complete Genomics), but a prescription is required. So I guess your vet could write a prescription for Fido the family dog...
OK, yes, "subtle" is probably a bit rough - I guess the last couple of years in genomics have trained me to view anything less than order-of-magnitude changes as insignificant. :-)
Regarding non-human sequencing: I have a feeling Illumina will be reluctant to do too much of this for the same reasons as Complete: when your informatics pipeline is optimised for one genome it can be surpisingly painful to switch to another one, especially for a one-off sequencing run. However, I'd imagine there are any number of biologists out there who'll be willing to test Illumina's willingness here, especially once the price drops a little lower!
IS personal genomics the new mantra? There are many companies coming up in the next few months that are investing in this. WHO will be the best among them? WIll Navigenics and 23andme woo the market?
An equally interesting effect will be to see how much stimulus money (ie, SIGs) increases the total number of sequencers in the coming year. Service providers and acedemia will be flush with instruments needing projects as consumable costs keep coming down and throughput increases.
U of Michigan now has its first ABI solid to compliment the three GA's on campus.
Great piece, Daniel. I'd hoped to write about this for the paper yesterday but got sucked into swine flu.
I agree that while the cost cut is sharp, it's still way about the level that's affordable to anyone other than millionaires. A little experiment on this has occurred to me: I wonder what the threshold is at which my editors will agree to have me sequenced for a story...? $5,000 maybe? Even that might be a bit steep.
You're right of course that most people will need their genomes sequenced just once, and that interpretation will be the interesting (and lucrative) bit. But that doesn't necessarily mean that that sequencing will be a completely insignificant market.
Even if you're charging as little $100 a time, 300m people in the US and 500m in the EU adds up to a lot of dollars, with new customers born all the time. Childhood vaccines are generally a one-off event too, but there are good profits to be had (if not on the scale that Jenny McCarthy & friends like to imagine...!)
I've posted a further thought on this on the Science Central blog at Times Online...
I like the idea of the "editor spend" test as an indicator of the affordability of genome sequences - let me know how that goes!
I do totally agree that sequencing itself will be lucrative given the sheer number of people to be analysed. My argument is mainly that companies offering interpretation as well as just raw data will have many more opportunities to distinguish themselves from the competition, rather than just the simple axes of speed, accuracy and cost.
Since I expect that Illumina will likely dominate the WGS market over at least the next year or two, they have a clear opportunity to link themselves in the public mind with the whole process of analysing a genome sequence rather than just the sample-handling and data generation steps., and I think they should take it!
The Fate Institute believes that the more personal genome sequencing companies choose to invest in interpretations of SNP data as well as the technology the easier it will be for individuals to be able to choose how and by whom they want their future to be interpreted.
Those start-ups and corporations who interpret their future each have their own motivations, branding and perspectives that taint the outcomes.They currently offer interpretative services that offer individuals a subscription to a fountain of their own self-knowledge that will continue to provide analysis about their own future lives indefinitely.
However how will this change as the technology develops further and becomes accessible to all?
What will be the impacts of an open source democratic approach to personal genome sequencing?
How will this technology be harnessed if it leaves the large private sector laboratories and enters individuals homes and makeshift laboratories similar to those that are occurring in response to the synbiobrick era?
Will citizen geneticists be able to sequence their genome and interpret the data in their own home, patent it using Science Commons licenses and sell their services on ebay or Amazon?
What similarities and differences can we see between this possible future and the open source approach in the software industry and the abilities for the web 2.0 to provide platforms for amateur activists and social entrepreneurs that exists outside of traditional corporations, start ups or top down state structures?
Wouldn't this be about 10 60bp runs on the GAII?
From what i've heard the reagents alone would add up to about 50k. I guess they wouldnt cost that much for illumina, still a very low price at this point.
When the company i work for was first starting out, we did work below cost for one special customer as a way to defray costs of optimization.
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