With the publication last year of its strategic plan, “Forging the Future — A Ten-Year Strategic Vision” the U.S. Department of Energy Joint Genome Institute (DOE JGI) has positioned itself to provide the most current technology and expertise to their users so that they can address pressing energy and environmental scientific challenges.
An important early step in this process is the launch of the Emerging Technologies Opportunity Program (ETOP). The primary purpose of the ETOP is to develop and support selected new technologies that DOE JGI could establish to add value to the high throughput sequencing it currently carries out for its users. The program was one of several recommendations that emerged from the DOE JGI’s strategic planning as well as a complementary process carried out by DOE’s Office of Biological and Environmental Research. Now, a new set of partnerships is taking shape in response to the ETOP’s first call for proposals. These span the development of new scalable DNA synthesis technologies to the latest approaches to high throughput sequencing and characterization of single microbial cells from complex environmental samples.
Photo: One of the challenges to be addressed via the ETOP effort relates to the assignment of genome fragments (represented by dots) to genomes (represented by clusters of colored dots, separated from adjacent clusters by dark barriers). Here a subset of data from a complex sample was analyzed. Sequence compositional information was used to generate clusters in an emergent self organizing map (ESOM). (B. Thomas and J. Banfield)
“A core philosophy of the DOE JGI is that our suite of technical and analytical capabilities needs to evolve continuously so that the scientific achievements of our users can be maximized,” said Jim Bristow, who oversees the ETOP as DOE JGI’s Deputy Director of Science Programs. “This occurs by building new scientific capabilities at the DOE JGI itself, and by enlisting partners, like the ones we’ve identified through this program, to develop and deploy highly-specialized technologies that complement activities at our Walnut Creek facility. While state-of-the art massive-scale sequencing remains a critical component of the DOE JGI, other large-scale capabilities particularly those that will help link sequence to function will be provided to JGI users in the future,” Bristow said.
When the DOE JGI was founded back in 1997 to help accelerate the Human Genome Project (HGP) effort, the partnership consisted of DOE National Laboratory and university partners. After completing the DOE’s commitment to the HGP in 2004, the DOE JGI opened its doors as a national user facility advancing the frontiers of genomics for energy and environmental applications. In 2012 alone, the Institute completed over 2,600 projects.
Photo: Microfluidic device involved in high-throughput sorting of microbial cells. (Roman Stocker)
For the first cycle of the ETOP, the DOE JGI has selected these six new partnerships:
- “Single cell approaches to metagenomics,” proposed by Stephen Quake of Stanford University. This technology could make it easier to isolate single cells of interest from complex environmental samples.
- “Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules,” proposed by Jay Shendure of the University of Washington. This technology could streamline the DNA synthesis pipeline and increase the output.
- “High-throughput sorting of microbial cells with specific functional traits for single cell genomics by combining labeling with heavy water, Raman microspectroscopy, microfluidics and flow cytometry,” proposed by Roman Stocker of MIT and Michael Wagner of the University of Vienna (Austria). This technology could accelerate the functional characterization of genes from metagenomic sequencing experiments, one of DOE JGI’s highest priorities.
- “Generation of high-quality genomic DNA from plants and other organisms, large insert libraries and high-quality physical maps for improved physical map and sequence level-assemblies,” proposed by Rod Wing of the Arizona Genomics Institute (AGI). This technology could make considerably easier the isolation of DNA from plants in amounts and quality that can be more effectively sequenced by the DOE JGI.
- “Development of a pipeline for high-throughput recovery of near-complete and complete microbial genomes from complex metagenomic datasets,” proposed by Jill Banfield of the University of California, Berkeley and Lawrence Berkeley National Laboratory, Chongle Pan of Oak Ridge National Laboratory, and Brian Thomas of the University of California, Berkeley. This technology could result in better methods for isolating and characterizing entire microbial genomes from the fragmentary sequences typical of environmental samples.
- “Development and Implementation of High Throughput Methods for Fungal Culturing and Nucleic Acid Isolation,” proposed by Jon Magnuson of Pacific Northwest National Laboratory. Similar to the AGI proposal above, this technology could make the isolation of DNA from fungi in amounts and quality that can be more effectively sequenced by DOE JGI considerably easier.
The DOE JGI expects to commit approximately $3.5 million over the next two years to the new ETOP initiatives.
“The DOE JGI strives to integrate these expanded activities in innovative and effective ways,” said Bristow. “This is critical if the biological sciences are to realize the full benefits and promise of genome sequencing.”