Although the sequence of the human genome was substantially completed in 2002, there is still a huge need for the production of DNA sequence data. In particular, the genome within carcinogenic tissues is believed to vary widely from a normal genome, both in inherited mutations and those caused by the disease. The NCI has recently set a goal of sequencing 12,500 genomes from malignant tumors of different individuals in order to learn more about the molecular basis of the disease. To cost effectively reach this goal, new technologies for DNA sequencing will be required. We propose to use the sequencing by synthesis (SBS) method as the basis for a prototype instrument which will be capable of effectively sequencing genomes from highly mutated tumor tissues. When fully optimized, our system should be able to produce read lengths which are at least as long as today's state-of-the-art electrophoresis-based systems. This may become a critical parameter for cancer genomes which have undergone sufficiently complex mutations that will make accurate assembly of short re- sequencing data difficult. In this Phase I SBIR project, we propose to develop the sample preparation approach which will simplify the SBS steps and make the process more robust for long sample reads and could be implemented on hundreds of thousands or millions of samples. Successful accomplishment of the Phase I milestones and completion of a subsequent Phase II and Phase III projects will result in the development of an ultra-high throughput system which can produce cost-effective high-density chips for use in conjunction with advanced DNA sequencing instruments. Ultimately, this next generation of sample preparation and sequencing technologies, which can produce DNA sequence several orders of magnitude cheaper and faster than existing systems, can help give researchers more insight into the molecular mechanisms of cancer and make the promise of individualized treatments a reality. Project Narrative: Ultimately, the ability to produce very inexpensive detailed DNA sequence information for complex organisms genomes will both lead to accelerated discoveries throughout biology and provide the basis for Pharmacogenomics, a new paradigm in therapeutics wherein medicines are prescribed based on individual genotypes rather than just observed symptoms. A system which could inexpensively sequence the DNA within a specific tumor will help cancer researchers understand the mutations associated with various types of cancers and help lead to more effective treatments. Since one's genomic sequence never changes, it is likely in the future that everyone will have their genomes sequenced at birth, recorded electronically and used throughput their lifetime to customize their healthcare. ? ? ?
