SBIR-STTR Award

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. 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

The advent of next-generation sequencing technologies is allowing researchers to perform studies and make discoveries which previously were not economically or technically feasible. For example, precise knowledge of the genomic sequence within neoplastic tissues can be an indicator for treatment (similar to the erbB-2 receptor gene, Her-2, for breast cancer). Although much research and development effort has gone into the core chemistries and instruments which actually produce sequence data, few new techniques have been applied to the preparation of samples for high-throughput or use in the clinic. In particular, sequencing systems that use beads as both the solid support for amplification and to help localize samples on a sequencing chip still require tedious processing by hand. As labs scale up to use the new sequencing technologies, they are very quickly realizing that the bottleneck in the operation is in the sample preparation. In this Phase II application, we propose to take the sample preparation steps far beyond the original Phase I scope of library construction. We propose to automate the entire sample preparation process, starting just after DNA fragmentation, through library construction and ending just prior to attachment to a chip. The proposed system will be compatible with a number of next generation systems which are starting to enter the market.

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