Will the Democratization of Sequencing Undermine Openness in Genomics?

It is no secret, nor is it an accident, that the success of genome biology over the last two decades owes itself in large part to the Open Science ideals and practices that underpinned the Human Genome Project. From the development of the Bermuda principles in 1996 to the Ft. Lauderdale agreement in 2003, leaders in the genomics community fought for rapid, pre-publication data release policies that have (for the most part) protected the interests of genome sequencing centers and the research community alike.

As a consequence, progress in genomic data acquisition and analysis has been incredibly fast, leading to major basic and medical breakthroughs, thousands of publications, and ultimately to new technologies that now permit extremely high-throughput DNA sequencing. These new sequencing technologies now give individual groups sequencing capabilities that were previously only acheivable by large sequencing centers. This development makes it timely to ask: how do the data release policies for primary genome sequences apply in the era of next-generation sequencing (NGS)?

My reading of the the history of genome sequence release policies condenses the key issues as follows:

  • The Bermuda Principles say that assemblies of primary genomic sequences of human and other organims should be made within 24 hrs of their production
  • The Ft. Lauderdale Agreement says that whole genome shotgun reads should be deposited in public repositories within one week of generation. (This agreement was also encouraged to be applied to other types of data from “community resource projects” – defined as research project specifically devised and implemented to create a set of data, reagents or other material whose primary utility will be as a resource for the broad scientific community.)

Thus, the agreed standard in the genomics field is that raw sequence data from the primary genomic sequence of organisms should be made available within a week of generation. In my view this also applies to so-called “resequencing” efforts (like the 1000 Genomes Project), since genomic data from a new strain or individual is actually a new primary genome sequence.

The key question concerning genomic data release policies in the NGS era, then, is do these data release policies apply only to sequencing centers or to any group producing primary genomic data? Now that you are a sequencing center, are you also bound by the obligations that sequencing centers have followed for a decade or more? This is an important issue to discuss for it’s own sake in order to promote Open Science, but also for the conundrums it throws up about data release policies in genomics. For example, if individual groups who are sequencing genomes are not bound by the same data release policies as sequencing centers, then a group at e.g. Sanger or Baylor working on a genome is actually now put at a competetive disadvantage in the NGS era because they would be forced to release their data.

I argue that if the wider research community does not abide by the current practices of early data release in genomics, the democratization of sequencing will lead to the slow death of openness in genomics. We could very well see a regression to the mean behavior of data hording (I sometimes call this “data mine, mine, mining”) that is sadly characteristic of most of biological sciences. In turn this could decelerate progress in genomics, leading to a backlog of terabytes of un(der)analyzed data rotting on disks around the world. Are you prepared to standby, do nothing and bear witness to this bleak future? ; )

While many individual groups collecting primary genomic sequence data may hesitate to embrace the idea of pre-publication data release, it should be noted that there is also a standard procedure in place for protecting the interests of the data producer to have first chance to publish (or co-publish) large-scale analysis of the data, while permitting the wider research community to have early access. The Ft. Lauderdale agreeement recognized that:

…very early data release model could potentially jeopardize the standard scientific practice that the investigators who generate primary data should have both the right and responsibility to publish the work in a peer-reviewed journal. Therefore, NHGRI agreed to the inclusion of a statement on the sequence trace data permitting the scientific community to use these unpublished data for all purposes, with the sole exception of publication of the results of a complete genome sequence assembly or other large-scale analyses in advance of the sequence producer’s initial publication.

This type of data producer protection proviso has being taken up by some community-led efforts to release large amounts of primary sequence data prior to publiction, as laudably done by the Drosophila Population Genomics Project (Thanks Chuck!)

While the Ft. Lauderdale agreement in principle tries to balance the interests of the data producers and consumers, it is not without failings. As Mike Eisen points out on his blog:

In practice [the Ft. Lauderdale privoso] has also given data producers the power to create enormous consortia to analyze data they produce, effectively giving them disproportionate credit for the work of large communities. It’s a horrible policy that has significantly squelched the development of a robust genome analysis community that is independent of the big sequencing centers.

Eisen rejects the Ft. Lauderdale agreement in favor of a new policy he entitles The Batavia Open Genomic Data Licence.  The Batavia License does not require an embargo period or the need to inform data producers of how they intend to use the data, as is expected under the Ft. Lauderdale agreement, but it requires that groups using the data publish in an open access journal. Therefore the Batavia License is not truly open either, and I fear that it imposes unnecessary restrictions that will prevent its widespread uptake. The only truly Open Science policy for data release is a Creative Commons (CC-BY or CC-Zero) style license that has no restrictions other than attribution, a precedent that was established last year for the E. coli TY-2482 genome sequence (BGI you rock!).

A CC-style license will likely be too liberal for most labs generating their own data, and thus I argue we may be better off pushing for a individual groups to use a Ft. Lauderdale style agreement to encourage the (admittedly less than optimal) status quo to be taken up by the wider community. Another option is for researchers to release their data early via “data publications” such as those being developed by journals such as GigaScience and F1000 Reports.

Whatever the mechanism, I join with Eisen in calling for wider participation for the research to community to release their primary genomic sequence data. Indeed, it would be a truly sad twist of fate if the wider research community does not follow the genomic data release policies in the post-NGS era that were put in place in the pre-NGS era in order to protect their interests. I for one will do my best in the coming years to reciprocate the generosity that has made Drosophila genomics community so great (in the long tradition of openness dating back to the Morgan school), by releasing any primary sequence data produced by my lab prior to publication. Watch this space.

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5 thoughts on “Will the Democratization of Sequencing Undermine Openness in Genomics?

  1. Links 5/14/12 | Mike the Mad Biologist

  2. Reading list: read | Annotary

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