NEW YORK (GenomeWeb News) – The US Department of Energy Joint Genome Institute will position itself as a venue for carrying out larger-scale genomic sequencing projects in the coming year, administrators told GenomeWeb Daily News.
JGI said its action follows the exponential increase of its sequence output in recent years. Just over the past year, the institute's sequencing output has leapt to 6 terabytes, up from 1 terabyte at the end of the 2009 fiscal year.
"We're really interested in undertaking projects that either require specific upfront molecular biology, very large scale, or informatic capabilities that exist at the JGI and that won't exist in other centers," Jim Bristow, JGI's deputy director of programs, said earlier this month.
"We're not receiving a lot of single isolate microbial genomes for sequencing now, usually because people aren't interested in single microbes," Bristow said. "They're interested in collections of microbes. So increasingly that's what we're naturally seeing. Why ask for one when you can ask for 12?"
JGI signaled that directional shift this fall when it unveiled its 2011 Community Sequencing Program of 35 projects selected for follow-up by the institute. At the time, JGI urged researchers to submit proposals for projects that advance capabilities in fields such as large-scale resequencing, as well as in single-cell genomics, and metatranscriptomics.
The 35 CSP projects use most of the DOE JGI's increased sequencing capacity, allocating 10 terabases, a 30-fold increase from last year.
"Pretty significant" sequencing efforts have also been undertaken as part of ongoing pilot sequencing programs. One is the Genomic Encyclopedia of Bacteria and Archaea, which focuses on microbial diversity in the biosphere, and is being carried out by JGI with Germany's DSMZ. Another is the Great Prairie Soil Metagenomes Project that JGI is piloting for the DOE Grand Challenge Program, with the goal of understanding its complexity, both when cultivated and as native prairie grass.
"We're learning in the context of those very large projects how to get lots of samples in the door, how JGI can serve a leadership role in nucleating communities around large-scale genome projects," Bristow said.
Asked if he foresees JGI limiting sequencing projects to a minimum size, Bristow replied: "It's hard to say. I think that will occur by itself. When it's easier to walk down the hall and get an individual microbial isolate sequence than it is to go to our proposal process and send us the DNA, that'll probably happen."
Ray Turner, head of JGI's operations department, added during the interview with GWDN that JGI is "evaluating our needs for FY '11" with respect to sequencing platforms. In October, JGI retired its last Sanger sequencers after a decade of service, leaving it entirely with next-generation machines. The institute, at deadline, was evaluating options for what to do with some 20 of the Sanger platforms it had on site.
In regards to JGI's budget, Turner said it is "waiting to see like everybody else" whether the institute will secure the $69.3 million proposed for it earlier this year under President Obama's proposed budget for the 2011 fiscal year that began Oct. 1, part of $322 million in spending contemplated for DOE's Biological Systems Science Research effort. In its current lame-duck session, Congress has relied on continuing resolutions to preserve funding for programs at FY 2010 levels pending agreement on a FY '11 spending plan.
The budget outcome will determine decisions on whether to add to JGI's faculty or staff, Bristow added.