We propose to further develop and utilize ultra-high throughput polony genome sequencing with the primary goal of generating raw data to re-sequence the human genome in about one week (including library prep and sequencing) for less than $1,000. Currently, the technology is well advanced, but further progress is needed to meet our goals. As the critical quantitative milestone of the project, we will report the sequence for a human genome with "a target sequence quality equivalent to or better than that of the mouse assembly published in December 2002 (Nature 420:520, 2002)". The project is divided into four specific aims, which are to (1) increase the polony sequencing read length using a cyclic ligation strategy that involves enzymatic cleavage, (2) improve the library construction and emulsion protocols, (3) increase read density by moving to alternative clonal amplification strategies (other than emulsion PCR or ePCR), and (4) extend our software capabilities to allow SNP calls from our new proposed sequencing raw data. Progress towards our goals is at an advanced stage. We are able to routinely sequence bacterial genomes and we are on the verge of sequencing an entire human genome to the required quality level. Overall, we feel that there are substantial rewards to be gained by pursuing the goals described herein. We have extensive experience with the proposed technologies and we have a clear path toward the $1,000 genome.
Herein we propose to further develop and utilize Polony Sequencing Technology with the primary goal of sequencing the human genome in about one week at a cost of less than $1,000. We propose several approaches that will progressively move us toward and beyond the $1,000 human genome. We firmly believe that polony sequencing technology, as proposed, can achieve the $1,000 genome goal and undoubtedly revolutionize medicine.
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