Equal opportunity genomics

ScienceDaily reports a bold strike against the human genomics patriarchy:

Geneticists of Leiden University Medical Centre (LUMC) are the first to determine the DNA sequence of a woman.

Well, there are other female genomes out there - the 1000 Genomes Project has already generated moderate-coverage sequence for at least one female (an anonymous woman of European ancestry, collected in Utah) and low-coverage sequences of perhaps half a dozen more, and I think the Cancer Genome Project has sequenced at least one tumour sample from a female patient - but perhaps Leiden beat them to it, and at the very least they can legitimately claim to be the first to realise that the gender of a genome donor by itself was enough to warrant publicity.

Public relations aside, there's nothing hugely biologically interesting about sequencing a female genome - it just means you get one extra copy of the X chromosome. As the article notes, that does give us a little bit of extra information about the genetic diversity on this exquisitely interesting chromosome, but I'm not sure to what extent this outweighs the extra information you could get from sequencing a male (Y chromosome sequence, and accurate information about the precise arrangement of variations along the X chromosome - information that is "scrambled" when you sequence two copies at once).

The article is more interesting in what it says about the sudden explosion in sequencing capacity resulting from next-generation sequencing technologies:

"The sequencing itself took about six months. Partly since it was run as a ‘side operation’ filling the empty positions on the machine while running other projects. Would such a job be done in one go, it would take just ten weeks".

That's right - they sequenced an entire human genome using just the left-over capacity of their sequencing machines, in six months. This sort of capacity certainly isn't limited to Leiden: sequencing facilities around the world are all churning out human genome equivalents every few days. Now, consider that the first human genome took the combined work of hundreds of scientists from over 18 countries for thirteen years, and you have you a taste of how rapidly sequencing technology is moving.

I wonder how many more "first" human genomes we'll be expected to applaud over the next few months. Already this year we've had the first Nobel prize-winning genome, the first African genome and the first East Asian genome announced. Next, I suppose we'll have a spate of disease genomes: the first cancerous genome of course, but also perhaps the first autistic genome, the first obese genome, the first arthritic genome...

None of them will mean much by themselves; the exciting results will come when this exploding sequencing capacity allows researchers to compare the whole genomes of thousands of disease patients with those of thousands of controls. These studies are approaching rapidly, and in addition to their powerful information they'll bring a host of technical challenges in terms of sequence generation, data storage and transfer, and interpretation. I'll be talking a lot more about the promises and challenges of next-generation sequencing over the next couple of months - stay tuned.

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