We propose to develop a low-cost 10-Gb Pyrosequencer for de novo DNA sequencing that would enable any lab to perform high-throughput genome analyses. The platform implements automated sample preparation scheme combined with massive Pyrosequencing, which will potentially enable mammalian genome sequencing in a single run. A sensitive CMOS image sensor has been designed and fabricated specialized for Pyrosequencing chemistry, which is integrated with fluidic platform. Each well in the fluidic platform has a pixel on CMOS for detection of light signal generated from Pyrosequencing. The integrated chip will have a 2-megapixel CMOS, each pixel located on a single well enabling 2 million sequencing on each chip. Sixteen of such chips are set up on a board to develop a 32-million wells Pyrosequencer which potentially enable sequencing of more than 10 gigabase of genomic DNA. The raw data are immediately collected and assembled with our developed algorithms. We envision that the genome sequencing of mammalian genome to be reduced below $100,000 level for large-scale genome sequencing projects. PROJECT
This proposal aims to develop a new technology enabling rapid and high throughput DNA sequencing at any lab or clinic. This technology would have direct impact on rapid and accurate diagnosis, identification of new drug target, rapid environmental monitoring and would enhance our understanding about biological systems.
| Doostzadeh, Julie; Shokralla, Shadi; Absalan, Farnaz et al. (2008) High throughput automated allele frequency estimation by pyrosequencing. PLoS One 3:e2693 |
| Sundquist, Andreas; Ronaghi, Mostafa; Tang, Haixu et al. (2007) Whole-genome sequencing and assembly with high-throughput, short-read technologies. PLoS One 2:e484 |
| Mashayekhi, Foad; Ronaghi, Mostafa (2007) Analysis of read length limiting factors in Pyrosequencing chemistry. Anal Biochem 363:275-87 |
| Ronaghi, Mostafa; Shokralla, Shadi; Gharizadeh, Baback (2007) Pyrosequencing for discovery and analysis of DNA sequence variations. Pharmacogenomics 8:1437-41 |
| Sundquist, Andreas; Bigdeli, Saharnaz; Jalili, Roxana et al. (2007) Bacterial flora-typing with targeted, chip-based Pyrosequencing. BMC Microbiol 7:108 |
| Parameswaran, Poornima; Jalili, Roxana; Tao, Li et al. (2007) A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res 35:e130 |
| Agah, Ali; Aghajan, Mariam; Mashayekhi, Foad et al. (2004) A multi-enzyme model for Pyrosequencing. Nucleic Acids Res 32:e166 |
