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Monday, February 2, 2009

two steps forward to realize you haven't gone anywhere...

I'm still trying to finish off my AGBT poster, which is a scary thought. AGBT starts Wednesday, and I haven't sent off anything to the printers yet. In fact, until about 5 minutes ago, I was still processing the raw data. At any rate, it only takes a few minutes to re-generate all of my figures (yay for automating processes), so I know what all of them (except for the two most complex) will look like.

After spending the whole weekend working on this, as well as a significant investment in time over the past week, most of the figures have barely changed. Woo! Adding 5 more cell lines (samples, really), hasn't done much to change things. I suppose that's a direct consequence of the law of diminishing returns, and clearly the returns are diminishing. Of course, that could also be a consequence of the complete lack of saturation of the sequencing of the 5 added samples, but I don't think people want to deal with that yet...

In fact, that's probably one of the biggest issues in genomics: we all want to get the best results with the least investment, and with genomes, the investments are big. To really ensure that the results are the best they could be, I'd have to get several more flow cells of data from each of these new samples.

And, that brings us right back to the question that was asked at several panels at last year's AGBT: How much sequencing is enough. My favorite answer, last year, was "it won't be enough until we've sequenced every person on the planet." Unfortunately for my poster, we're a LONG way from that. But again, how much will we really learn from sequencing the 6 billionth person? I can't imagine it's worth the time or investment by that point. (By the way, if we wanted to do the same thing for some species, such as bow whales, you'd have to stop around the 8000th individual - since there aren't any more than that. There are 750,000 people on the planet for every bow whale left! But i digress...)

In light of my results, I am rethinking the "how much is enough?" question. Given what I saw today, probably a few 1000 is more than enough, but then again, you have to ask "enough for what?"

For personalized medicine, the answer is clearly going to be to sequence everyone who gets health care (which we hope is everyone.) Unfortunately, the technology required to do that is a long way from where we are now. (Although, we did see some very promising technologies at AGBT last year.) For my poster, though, I wonder if I already have enough to do what I need to. There's my two steps forward... and the realization that taking those two steps probably didn't add much.

You'll notice I also mentioned AGBT a few times in today's post - and some of the reasons why I'm looking forward to another year of intense genomics discussions. New technologies, new methods and discussions with other scientists on where the field is going... and, of course, a lot of opinions on how we're going to get there.

And one thing I didn't mention. In the course of realizing I hadn't gotten any further forwards with my new results, I discovered a few interesting steps sidewise. Isn't that just like science? If you keep your eyes open, you'll find things you weren't looking for. (=

I'm sure there will be lots of surprises at this year's AGBT too.


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