Mailund on the Internet

If you want your very own genome sequenced, you know have the chance for just $48,000.  Not only will Illumina sequence the genome for you, at 30X coverage, they’ll throw in a Mac for you to store it on.

Read much more about it here:

• GenomeWeb: Illumina Launches Personal Genome-Sequencing Service Using Genome Analyzer II
• Genetic Future: Illumina launches personal genome sequencing service for $48,000
• Forbes: Genomes! Get Your Genomes! Just $50K

This is both exciting, and then also not so much…

Personal genomics with actual sequencing is exciting.  Companies like DeCodeMe and 23AndMe only genotypes selected common variants.  About a million of them, so covering the genome quite well, but far from the (two times) three billion nucleotides in the full genome, so not likely to capture the rare variants in your genome.

Providing the full sequence is also what Knome does, but while Knome will charge you $99,500, Illumina will only charge you $48,000 (and throw in a Mac).

Of course, the price is what makes it less exciting.  While Illumina’s offer is half the price of Knome, it is still far from DeCodeMe (1M markers for $1000) or 23AndMe (500K markers for $400) and not really in the range of the average citizens.

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Years back, when I was studying computer science, I took a course on virtual machine design by Lars Bak.  At the time he had just returned to Denmark but was still working at SUN and he managed to get a VP from SUN to give one of his lectures for him (I forget who it was, as I said it was many years ago).

That particular lecture wasn’t about building object oriented virtual machines but about building successful software companies.  (No snide remarks about someone from SUN talking about that, please).

This was during the .com bubble or just while it was bursting, and the advice he gave was: “when everyone is digging for gold, you get rich by selling shovels”.

If you build the basic infrastructure that everyone needs, it might not be as glamorous and if you are selling commodity products you won’t get rich over night, but if you are selling something that everyone needs, you won’t loose your market over night.

Personal genomics and medicine shovels, anyone?

I’m telling this story because I just read this post at Genetics Future. It concerns genetic testing and how it will soon change with complete re-sequencing which will be cost-effective Real Soon Now(tm).

The post ends:

There are ruthless economies of scale in the human disease genomics business, both in terms of sequencing infrastructure and the costs of assembling reliable knowledge bases for interpretation, so it will be increasingly difficult for smaller companies to stay competitive.

The personal genomics and genetic testing field is another gold rush (although one where small garage companies aren’t quite in on the game yet).  Right now there’s plenty of testing labs, but with resequencing we’ll probably only get a few large companies, at least until the price for resequencing drops significantly.

I don’t want to compete here.  I’m sure I’ll lose.  I would absolutely love to be selling shovels to the gold diggers!

What will all these companies need?

Of course they will need IT infrastructure to manage their data and statistical methods to correlated genotypes with phenotypes.

The question is, of course, whether it will be possible to sell bioinformatics to such companies, or whether they will want to build all their informatics in house.  Some, they want to, of course, as that will give them a competitive advantage, but surely there will be some commodity software they will want to buy somewhere else.

They won’t build their own OS or database system, but probably their own specialised statistical models. Somewhere in between, there is money to be made, if I can only figure out how…

At Think Gene, Andrew Yates has a review of 23andMe.  Mainly about the web interface — that does look cool — but then he concludes:

The Disappointing

Of all the 70 possible traits described by the 23andMe test, no trait reported anything useful except perhaps a moderate (almost 30%) risk of rheumatoid arthritis.

The sad fact is that, for common SNPs, all risks we know of are small to moderate.  If we knew how they interacted, maybe we could detect higher risks, but right now we only see small increases in risk in the SNPs we know about.

If you expect more, you will be disappointed indeed.

I think personal genomics is pretty cool, but I doubt it has any clinical relevance at this point.  I could be wrong, of couse, but that is where I would place my bet.

I just stole these videos from Eye on DNA – sorry Hsien — ’cause I wanted to share them here.

I just saw this deCODEme add on Eye on DNA:

It was a bit funny seeing the place I’ve visited so often on YouTube, and to see people I’ve met up there describe deCODEme. (I’ve had some discussions with Agnar and talked to Hakon a few times, but my work when I’m visiting DeCODE is not involving them so I do not know them that well, but still).

My work there has nothing to do with deCODEme, though, but with genome wide association mapping. You can read about it on the PolyGene homepage.