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What is it with rich white guys and genome sequences?

By dgmacarthur on August 11, 2009.

David Dooling has an entertaining take on the Helicos genome sequence I discussed yesterday entitled "Another rich white guy sequences own genome". 

I noted in my post yesterday that the alleged price drop for the Helicos sequence over current technologies was an illusion, but David includes a much more thorough analysis of the relative genome sequencing costs thrown around over the last couple of days and makes it very clear that the price Helicos is quoting is really no advance over the current prices for second-generation sequencing technologies:

They report reagent costs that are on par with current second generation technology fully loaded costs (which are closer to $50,000, not the $250,000-$500,000 they report in their letter). Yes, you read that right, their reagent costs alone are on par with reagents, instrument depreciation, personnel, and IT infrastructure for second generation platforms. Quake does report in an interview that the amortized equipment cost was $10,000-$20,000. Assuming a straight line depreciation for the Helicos instrument, a $10,000-$20,000 depreciation over four one-week runs yields a $125,000-$250,000 annual depreciation. Their first instrument was sold for $963,000 and they subsequently lowered the price by 25%. So assuming their price now is $725,000 and the residual value of the instrument is $0 (not a bad assumption given the pace of change in this industry), they are estimating a life of their instrument of about three to six years. Again due to the pace of change of this industry, even three years may be generous.

It's a real shame that reporters who should have known better (e.g. Nicholas Wade), as well as the reviewers on the paper, allowed Quake to get away with the claim that the cost of a Helicos sequence represents a genuine improvement over the current state of the art. As for the pointless comparison between the cost of the first ever genome sequence and the Helicos effort (courtesy Gizmodo, headline "Genome Sequencing Gets 99.9833% Price Cut") - well, the less said about that the better.
On an unrelated note, sequencing afficianados may well also enjoy David's pointer to a letter from Life Technologies' Kevin McKernan to a recent UK House of Lords committee, which is unintentionally hilarious on a number of levels - and in fact really has to be read to be believed.
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helicos
next-generation sequencing
whole-genome sequencing
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Technology

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I'm hardly qualified to defend Helicos, but my understanding is they're still only using part of their flowcell and could still increase strand density substantially. Thus, yes, it's possible the residual value of the instrument will be $0 in five years, but my understanding of the Helicos business model is that the HeliScope platform is supposed to be expandable. That said, obviously this has no bearing on the cost of sequencing a genome today.