Geospiza Awarded Phase 1 Research Grant by NIH to Investigate Applications for Integrating Optical Mapping with DNA Sequence Assembly
Geospiza announced that it has been awarded a 6-month, $100,000 Phase I Small Business Innovative Research (SBIR) grant from the National Institutes of Health (NIH), in collaboration with OpGen, Inc. The grant will fund the investigative phase of a plan to build a genomic sequencing and assembly tool that incorporates optical mapping data to help improve analysis efficiencies and further drive down the cost to produce each personal genomic profile.
While Geospiza is primarily known for its Finch Sequencing Center software for managing and processing the results of large-scale genome sequencing projects, the research arm of the company has also been engaged in a long-term project to bring the popular sequence assembler Phrap up to date for modern assembly needs. Geospiza is currently completing another $1.1 million SBIR grant to re-engineer Phrap, which is providing a solid foundation for the development of an “Optical-Map Phrap” application.
Geospiza collaborator OpGen is a biotechnology company focused on bringing its unique Optical Mapping technology to market. OpGen Optical Mapping is a single-molecule DNA analysis technology that provides the first commercially practical, cost-effective method for whole-genome analysis in large populations. The company’s vision is to make the physical analysis of whole genomes in minutes a reality. Together, OpGen and Geospiza will be investigating the feasibility of incorporating the output of optical mapping as input to a DNA sequence assembly program.
“If the Phase I pilot study is successful, we hope to collaboratively initiate development of a kit that will allow scientists to simultaneously sequence and map the genome of their target organism much more quickly, yielding a confident picture of the final result,” said Dr. Christie Robertson, the project’s principal investigator.
Geospiza’s chairman and CEO, Todd M. Smith, Ph.D., added, “Obtaining physical map data for any new organism is a real challenge. Without these data, random sequences end up being blindly assembled, leading to error prone results. OpGen’s technology fills a critical gap in the DNA sequencing process and by using map data from their technology to guide sequence assembly in Phrap, sequencing productivity in many areas of basic and clinical research will increase.”
Dr. Colin Dykes, chief scientific officer and vice president of OpGen points out that optical mapping has a strong track record of use to order and orient large sequence contigs in several genome sequencing projects, including that of the fungal pathogen, Aspergillus fumigatus. “Now OpGen is working to develop a tool that will allow early integration of DNA sequence and optical map data to provide a system for more accurate, and cost-effective, sequence assembly,” he explained.
About OpGen
OpGen, Inc. is commercializing technology that will revolutionize modern medicine by providing the first means for rapid, cost-effective comparison of whole genomes in populations. Such whole genome analysis will enable practical pharmacogenomics, forensic microbiology, and whole genome molecular diagnostics. Optical mapping, the technology that makes this all possible, is the first and only publicly validated system for single DNA molecule analysis. OpGen, Inc. uses optical mapping to produce information across whole genomes in a single, cost-effective manipulation, with no requirement for prior sequence information, PCR, synthesis, cloning or probes. This information can be used for DNA sequence validation, comparative genomics, biodefense, and molecular diagnostics.
About Geospiza
Geospiza combines life sciences and IT expertise to deliver low-cost, high-productivity software systems to research teams and core labs worldwide. Geospiza’s integrated Finch system for DNA sequencing laboratory workflow, data management and analysis turns complex scientific processes into reliable, upgradeable and scalable every-day practices scientists and technicians can use to get their work done. Geospiza was founded in 1997 and serves more than 6,000 researchers in both established and emerging biotechnology, academic, government and bio-pharmaceutical companies worldwide. More information is available at www.geospiza.com .
