SBIR-STTR Award

Wide use of the shotgun DNA sequencing method for the acquisition of draft data is not followed by the equally productive finishing technology. We have recently combined our proprietary biochemical and chemical approaches and showed feasibility of rapid finishing of draft human BAC projects with 2.3x-4.5x coverage to the high quality and contiguity standards. Development of high throughput technology based on our methods will transform the art of finishing genome projects into a streamlined production operation. Our objective is the development of advanced DNA sequencing reagents and protocols that are 100 to 1,000 times more efficient than the current standards and apply them for the sequencing directly off BAC and genomic DNA templates. We will design a model for the optimization of the overall workflow in the high throughput environment and test it on the ongoing genomics projects. In Phase I we will demonstrate feasibility of our approach to multiply the yield of sequencing reactions. We will show how the advanced chemistry will simplify massive sequencing of BAC and microbial genomic DNA and make direct sequencing of larger genomes possible. We will also develop a new solution for sample tracking and internal control.

Commercial Applications and Other Benefits as described by the awardee:
Rapid and cost effective finishing of genome projects will fulfill unmet demand in academic and government projects and booming biotechnology industry. It will free genomics centers and companies from unproductive work and accelerate overall rate of data acquisition. Streamlined sequencing directly off genomic DNA without cloning or PCR steps will find wide applications in functional and comparative genomics.

The shotgun DNA sequencing method is in wide use for the acquisition of draft data, but it is not followed by equally productive finishing technology. High throughput technology is needed to transform the art of finishing genome projects into a streamlined production operation. This project will develop advanced DNA sequencing reagents and protocols that are 100 to 1,000 times more efficient than current standards and apply them for the direct sequencing of Bacterial Artificial Chromosome (BAC) and genomic DNA templates. This will be accomplished by designing a model to optimize overall workflow in the high throughput environment and test it on ongoing genomic projects. Phase I demonstrated the feasibility of increasing the yield of sequencing reactions. 10,000 Fimers were synthesized and applied for direct sequencing of BAC and microbial genomic DNA. The results showed that the direct sequencing approach was suitable for further development and implementation into large scale projects. Phase II will incorporate new enzymatic and chemical tools for more efficient sequencing of microbial genomic DNA, and overall workflow will be optimized for the high throughput environment.

Commercial Applications and Other Benefits as described by the awardee:
Rapid, cost effective finishing of genome projects should fulfill unmet demand in academic and government projects, as well as the booming biotechnology industry. It should free genomics centers and companies from unproductive work and accelerate the overall rate of data acquisition.