We propose to further develop and utilize ultra-high throughput polony genome sequencing with the primary goal of re-sequencing the human genome in under one week at a cost of less than $10,000. 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 basically to (1) to improve the polony sequencing technology by increasing the read length, improve the library construction protocol, and increase bead density in the sequencing reactions, (2) improve the design of the polony genome sequencing microscope, (3) improve the computational tools that we have for assembling the raw sequence reads, and finally, (4) re-sequence a cancer genome and identify the somatic mutations that have occurred during tumor development. 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. Additionally, we feel that there are substantial rewards to be gained by pursuing the goals described herein.
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