I think this is key, and I think it’s why we’ll see a slow fading of big genome centers in the coming years. More on my blog here:
http://www.chrisamiller.com/blog/2009/06/12/the-fading-of-big-genomics/

Group Calls for Rapid Release of More Genomics Data
Science 22 May 2009:
Vol. 324. no. 5930, pp. 1000 – 1001
http://www.sciencemag.org/cgi/content/summary/324/5930/1000-b

I’ve forwarded this URL (and Mike the Mad Biologists) to the “wordsmiths” …

This inaccurate quote sums it nicely for me:

F Scott Fitzgerald: The rich are different than you and me.
Ernest Hemingway: Yes, they have more money.

The genome sequencing centers are obligated to do much more than just generate raw data (as described in the post). It is also not accurate to say we are not concerned nor evaluated on publications. Nor are my concerns over whether large scale sequencing centers continue to “get more work”.

I do agree that the issue is much larger than I describe in the above post (admittedly due to lack of time). One of the main problems is that the enforcement of the Fort Lauderdale agreement has been sporadic at best. It relies on journal editors for enforcement but they suffer from similar perverse incentives and principal investigators: wanting to scoop one another.

There needs to be a common set of standards for similar types of projects and they need to be enforced through funding institutions.

I agree that most next-gen sequencing and medical sequencing projects do not fall under the provisions described by Bermuda/Fort Lauderdale, which is exactly the point. Most of what large genome sequencing centers are doing now are not the type of projects that were done five to ten years ago, i.e., not the type of projects that fall under Bermuda/Fort Lauderdale. The goals and end results of many of the projects are no different than those of single investigators. The only difference is the scale. So why should there continue to be a difference in submission policies?

Because the large centers are contracted to produce sequences and make them publicly available, while small researchers are given grants for particular areas of research.

A genome center, also, does not care about publications. As long as they provide the sequences they were paid for, in the time they promised, they’ll get more work.

If an individual researcher pays for sequencing something, pre-releases the sequences, and then gets scooped by another group (a larger one, or one that just happened to have a few people free to crunch the data faster then the researcher’s team could), that researcher’s career is toast. He won’t get funding again.

If we institute a policy that forces small researchers to pre-release, all we’ll get is that small researchers will stop sequencing and start relying entirely on data produced by large centers.

The only alternative is to reform the grant system, but how to do that is a whole different – and much larger – can of worms.

Because they’re not doing the same thing, nor for the same purpose?

The Bermuda principles were designed “to apply for all human genomic
sequence generated by large-scale sequencing centres, funded for the
public good, in order to prevent such centres establishing a privileged
position in the exploitation and control of human sequence
information”.

The Fort Lauderdale agreement stipulates that the pre-publication rules
should be extended to “other large-scale production centers”, but still
only to apply to “community resource projects” defined as those
“specifically devised and implimented to create a set of data, reagents
or other material whose primary utility will be as a resource to the
broad scientific community”.

Most next-gen sequencing and other medical research projects do not
fall under this definition, but instead are trying to answer rather
specific questions with the minimum (well-powered) set of data required
to do so. On-publication release of data – or even post-generation
release, of say, the control portion of the data as was the case in WTCCC – may be of more general
utility, but that is not why the project was funded: there is one key
analysis to be performed, and that by the group funded to do so.

However, this is in the funders’ court. If they asked:

“would you take this grant for your rather specific medical genetics
project only on condition of pre-release of all data?”

the answer would probably be a grudging, “well, if you insist” …