Again with Big Genomics

Since my last post, the question of why we need big genome centers has been bouncing around in the back of my mind. One commenter on that post said_

The reason is quality. A large center can (and in my experience does) perform much more quality analysis and produces more sequence more cheaply.

While I don't disagree, with sequencing price dropping dramatically, couldn't this be done just as well by one of the dozen or so commercial operations that now offer sequencing? They're all doing business on a large scale and this have just as much ability to offer quality product. Why should the NIH continue to subsidize something when it's being offered at reasonable rates from the corporate sector?

So no, I don't believe that big genome centers will be any better than industry at preserving read quality. As I said before, they will still be the ones helping to get next-gen sequencing platforms off the ground, but that's research, not providing a service. So what other advantages might they offer?

The idea that I've been kicking around is that they might offer a critical mass of talent in the same place. Instead of meeting twice a year at conferences, scientists work right down the hall from each other, and can thus bounce ideas off each other more quickly and easily. This probably also helps prevent duplication of effort. If you know Professor X next door is working on problem Y, you won't be wasting your time trying to beat him to the punch. Instead, you'll be contributing and collaborating with him.

That said, I think physical proximity and openness about research are quickly becoming less relevant, with the advent of online science. We can develop close-knit communities of researchers online and do more of our work in the open, which will actually help prevent scooping.

So how about it - what am I missing? What are your ideas for why big genomics centers can or will remain viable?


Written by Gribskov -

I don't think there is any such thing as an academic sequencing center. They are businesses that the federal government has (perversely) decided to support through research grants. That said, not-for-profit centers probably do much more research on new approaches/technologies and support a certain amount of speculative work that would not get done by for-profit companies. So if you want sequencing to continue to be used in novel ways, its probably good to have some. There is something to be said for the critical mass of talent idea. Part of the critical mass is people who are down-and-dirty with the technical details of the process. If all sequencing is contracted to companies, this will be lost to the university setting.

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