Monday, March 03, 2008

Genomics Blogger Dissed by the New York Times

Well, the New York Times has an article today on Knome, a company that is charging people $350,000 to have their genome sequenced. They have two people signed up so far. Amy Harmon, the author of the Times article, interviewed me by email for her article, mostly because I had blogged extensively about the recent AGBT meeting where many of these sequencing companies had presented their latest goodies. But alas, being a genomics blogger apparently does not carry as much weight as being (1) Jim Watson (2) someone who pays 350,000 to have their genome sequenced (3) running a genome center (Richard Gibbs) or (4) starting Knome (George Church). And so my quotes got left on the proverbial cutting room floor. Go figure.

Too bad for the Times, as I think I my quotes were pretty good. Although in all honesty, they would not have gone too well with the final article, which has some nice cohesion to it.

I should note that, other than the lack of my quotes, one thing that got left out of the Times article is any discussion of the quality of the genome sequence that will be provided by Knome. One would hope that 350K would buy a high quality genome sequence but it is unclear how good it will be. I note they claim they will provide analysis of the genome too, but as with other companies that cater to the rich and famous, details are limited on their web site.

This reminds me of a funny scene I witnessed involving Craig Venter and a wealthy friend of his. This was the day before Craig's personal genome was set to come out in PLoS Biology and the friend was asking Craig what it cost to sequence his genome. Craig said something to the effect of "man millions of dollars" and then Craig said, "but now it would cost only about 300K." The friend was intrigued. And Craig asked if he was interested and the friend, without seeming in any way to be joking, said, "sure sign me up." I guess, when money is abundant, why not get your genome sequenced? Maybe I should have told Harmon this story --- then I might have gotten in the Times.


  1. Distraught though I was to have to cut comments by you that were salient and, more importantly, pithy, I must take exception to the one you make here about my having failed to raise the issue of sequence quality. Since you provide more ample space than the New York Times for quotation, I include the relevant excerpt:

    "[...last fall, he got the DeCode SNP test for $1,000...]

    But Mr. Stoicescu was intrigued by the idea of a more complete picture. “It is only a part of the truth,” he said. “Having the full sequence decoded you can be closer to reality.”

    How close is a matter of much debate. Knome is using a technology that reads the genome in short fragments that can be tricky to assemble. All of the existing sequencing methods have a margin of error, and the fledgling industry has no agreed-on quality standards."

    I’d have liked to get into more detail, but ultimately the story was about not the technology but a cultural trend -- the emerging interest of the very rich in getting themselves sequenced – which your story about Craig’s friend certainly helps legitimize :-)

    Speaking of which Craig was also cut out of my story)!

    --Amy Harmon (aka, the disser)

  2. btw, just because space was tight in the NYT, I don’t see why the blog-reading public should be deprived of Jonathan Eisen’s comments on this subject…in an ideal world, there might have been a passage that read something like this:

    Jonathan Eisen, a geneticist at the University of California, Davis, who recently blogged about new sequencing technologies demonstrated at a scientific conference, compared the phenomenon to rich people paying $65,000 to be led up Mt. Everest.

    Except given the quickly-falling price of sequencing, “it would be like paying to go up Everest this year, if you knew that next year they were going to announce the fee would be $6 per person,’’ he said.

    And here’s the Craig passage, which I was also sad to lose:

    Knome is promising its first customers a free “upgrade” as the technology improves. But even highly accurate genome readings are likely to yield little information on an individual’s health or behavior until researchers can comb through tens of thousands of other genomes to identify the important differences among them.

    To that end, J. Craig Venter, whose genome was published last year in the open access journal PLoS Biology, appealed to Dr. Stoicescu and others in the genome jet set to make their sequences publicly available -- along with personal information about their disease susceptibility, drug response, appearance, mental and physical abilities that could help scientists deduce which genetic variants contribute to specific traits.
    “I applaud that level of pioneering,” said Dr. Venter, who is the founder of a nonprofit genomics institute that plans to sequence 10,000 human genomes over the next decade. “But if it’s kept private then it doesn’t help science.”

    -- Amy

  3. OK - you got me --- not only was I dissed from the original article but I could not even get an accurate diss back ... But hey, I guess that is what the blogger world is about.

  4. I guess the public has had enough of what a scientist has to say since they won't understand it or get it wrong anyway the interest might be more in the reasons for having one's genome sequenced so that if the man on the street strikes it rich will he wanna do that as well.


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