Roche Applied Science has chosen eight research projects — ranging from tissue regeneration in salamanders to social behavior of bees — that will receive a total of 2.3 gigabases of free sequencing under its One Giga-Base Grant program, In Sequence has learned. The company plans to announce the winners at this week’s Advances in Genome Biology and Technology meeting in Marco Island, Fla.
Roche kicked off the program, which set out to award one gigabase worth of free sequencing on 454 Life Sciences’ GS FLX to a scientifically interesting research project, in October. The company originally planned to make only one 1-gigabase award. However, a Roche official told In Sequence that because the number and quality of the proposals was so high, they opted to give away smaller amounts of sequencing to seven other projects.
The winning team, to receive one gigabase worth of sequencing at 454 Life Sciences’ facility in Branford, Conn., is a consortium of researchers at the Salk Institute in La Jolla, Calif., the University of California Irvine, and the University of Kentucky. They plan to study limb regeneration in the salamander Ambystoma mexicanum.
Second place goes to a group of scientists led by Loren Riesberg, a professor with a joint appointment in plant evolutionary genomics at the University of British Columbia in Vancouver and in biology at Indiana University Bloomington. He and his colleagues plan to use their 500 megabases of free pyrosequencing to study genetic changes that have made the yellow star thistle an especially invasive weed.
Another 300 megabases of sequencing will go to the third place winner, a research group led by Gene Robinson at the University of Illinois at Urbana-Champaign, which plans to study the genetics of social behavior in honey bees.
Five runners-up — four groups based in the US and one in Canada — will obtain 100 megabases of sequencing each for a variety of projects that range from biofuels to health-related studies.
The winning project, led by Wei Zhu, a postdoctoral research associate in Tony Hunter’s lab at the Salk Institute, seeks to identify regulatory regions of genes that are involved in repressing or activating chromatin in regenerating salamander limb blastemas via histone modification. The researchers will sequence DNA from chromatin immunoprecipitation experiments. Zhu’s team has no prior experience with 454 sequencing, and she believes that assembling the sequences will be a challenge since the salamander genome has not been sequenced yet. However, an EST database already exists. While this project could also be done by conventional sequencing, “it would be much more time-consuming and maybe more expensive,” Zhu told In Sequence by e-mail.
The second-place team plans to identify specific genetic changes that are associated with invasiveness in the yellow star thistle, “one of the world’s most noxious weeds,” according to Riesberg. To do so, they will perform multilocus genomic scans or “hitchhike mapping” of expressed sequences in many individual star thistle plants. That way, they are hoping to identify genes and mutations that have been the targets of selection in invasive thistle populations.
“This was not economically feasible without these next-generation sequencing methods.”
Next-generation sequencing “makes hitchhike mapping on a transcriptome-wide scale affordable,” Riesberg told In Sequence by e-mail “This was not economically feasible without these next-generation sequencing methods.” His lab already has experience with the 454 technology from a project that involved pyrosequencing of cDNA libraries from three sunflower genotypes, performed by 454.
Riesberg estimates that the thistle hitchhiking mapping project would have cost between $150,000 and $200,000 at 454 Life Sciences.
The response to the grant program, 133 applications in total from eligible teams in the US and Canada, “was greater than originally anticipated,” according to Tim Harkins, Roche’s marketing manager for genome sequencing.
Three experts reviewed the proposals, based on a scoring system they developed that took into account the scientific merit of the projects, their broader impact on society, and their ability to showcase the capabilities of the 454 technology. The reviewers were no strangers to the sequencing community: Elaine Mardis, co-director of the Genome Sequencing Center at Washington University Medical School; Stephan Schuster, a professor at Pennsylvania State University and an early 454 customer; and Rod Wing, director of the Arizona Genomics Institute at the University of Arizona.
In addition to goodwill, the 100-megabase projects of the five runners-up could also create more business for 454: they could generate preliminary data to submit with grant applications for government funding agencies, such as the NIH.
According to Harkins, Roche plans to renew the program and run it on an annual basis, increasing the winner’s award to more than one gigabase next time “to match the improvements to the system,” he said.