10,000 genomes – why?

In the genomics world that I inhabit, a consortium has just published an intriguing proposal to sequence the genomes of 10,000 vertebrate species. It’s described an article in the current Journal of Heredity – unusual in that this is not a research article, but a proposal. Nonetheless, the article is full of interesting facts about what we know (and don’t know) about vertebrate species and how they’re all related. It makes a good read for anyone interested in evolution; for example, how many people know that all vertebrates have a common ancestor who lived about 500-600 million years ago? Perhaps more interesting, evidence is emerging that we all share about 10,000 genes – which means that these 10,000 genes are so useful that their functions have been preserved for 500 million years.

The consortium is led by a number of outstanding scientists, including UCSC’s David Haussler and NIH’s Stephen O’Brien, both of whose work I like and have followed for years. And some aspects of this proposal are terrific: for example, they want to start collecting DNA now from 16,203 vertebrate species. This will make a great specimen collection for future work. (Heck, maybe I’ll even sign on to the project myself.)

But this proposal is more than that: it is also the opening salvo in an effort to raise $50-100 million for the sequencing of these species. The paper was announced with press releases and news articles in both Science and Nature, demonstrating that it is clearly a lobbying effort for new funding. Fair enough – science takes funding, and sometimes you have to build support for new ideas. However, given that two of the three leaders of the consortium are primarily funded by NIH, I can only guess at who they’re expecting to cough up the money. The NIH's human genome funding has been led by NHGRI, which continues to look for new ways to justify maintaining the size of its three enormous sequencing centers (the Broad Institute, Washington University in St. Louis, and Baylor College of Medicine). Now, let me say here that genomes are the bread and butter of my own work, and these centers have done terrific work for the past 10-15 years - and I've often collaborated with them. And I hope they will continue. But it hasn’t escaped my attention that the new NIH Director, Francis Collins, was a key force in building up those centers while he was Director of NHGRI, and we all know that the centers are near and dear to him.

But wait a minute: 10,000 genomes, none of which are human? Exciting idea, sure, but not for NIH. The NIH-led centers are already participating in the 1000 Genomes project, which is attempting to sequence 1000 individuals (at a low-level “draft” quality). If NIH wants to scale up, there are 6 billion more of us available. Admittedly, not everyone wants to have his/her genome sequenced, but plenty of us would be happy to volunteer. Take a look at the Personal Genome Project, which was started by George Church at Harvard, and is trying to sign up 100,000 humans to have their genomes sequenced.

So I’m going to be the skeptic here: if NIH is thinking of throwing its sequencing dollars at 10,000 more genomes, I suggest that it focus on humans rather than a broad collection of other vertebrates. (I know, this should be obvious, right? But sometimes NIH gets distracted.) We still have only scratched the surface of what there is to know about the human genome, and there’s plenty of DNA sequencing to do in the human population. The 10,000 genomes project sounds like a great mission for the National Science Foundation, which has ceded much of large-scale sequencing work to the NIH in the past 10 years, except for plant genomes and some bacteria. In fact, maybe this is a chance for NSF to have its own large-scale sequencing center – I’d be all for that. But I’m not at all convinced that NIH should spend its biomedical research dollars on 10,000 vertebrates. Let’s see how this plays out.