Name: Ying-Ja Chen
Email: yingja @ ucsd.edu
Grad Year: 2008
Genome sequencing is essential for biological research and clinical diagnostics. For example, the determination of complex diseases and individual variations between patients depends on the sequencing of populations. However, current sequencing technology is slow and expensive for genome sequencing due to the low-throughput of sequencing by capillary gel electrophoresis. To fulfill the increasing demand for genome sequencing, we are developing a technology for high-throughput genome amplification and sequencing that will provide several orders of magnitude improvement over the current technology. A method for massively parallel genome amplification is being developed. Billions of microwells are fabricated polydimethylsiloxane (PDMS) by standard techniques to accommodate millions to billions of amplification reactions. Target DNA clones could be amplified by rolling circle amplification (RCA) in these microwells. These amplified clones could be transferred to a solid surface for high-throughput sequencing technologies. A new sequencing strategy is being developed based on Sanger dideoxy sequencing reaction and denaturation. DNA products of different lengths are denatured sequentially and imaged on a surface to read out the sequence. Finally, an integrated system incorporating temperature control, microfluidics, and fluorescence imaging is constructed for automated sequencing. This method is straightforward and eliminates cycling reactions. Its ultra-high throughput will allow for the sequencing of the human genome on one device. In addition, an integrated system will provide the platform for conducting further experiments and applications, such as digital gene expression profiling, SNP detections, and so on. This work could make a great impact on biomedical research in the future.
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