Abstract

We propose the development of the Pyrosequencing array for genome sequencing. Pyrosequencing has widely being used by other laboratories for de novo sequencing and has a great potential for miniaturization.
The aim of this proposal is to develop an exportable inexpensive device that is able to produce sequence data of million of features on a single chip. As a multidisciplinary team at Stanford University, we have already worked toward the development of such a platform. The team proposes a plan to develop this methodology to reduce the cost below $100,000 for mammalian genome sequencing. We will discuss a step-by-step development plan to achieve this goal in three years. Briefly, the proposal covers clonal amplification, miniaturized Pyrosequencing, integrated PCR, Pyrosequencing platform, an integrated fluidic and CMOS imaging platform including a signal processing unit, automation of an inexpensive platform and methodology for short read assembly to assemble a mammalian genome. ? ?

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
5R01HG003571-03
Application #
7075346
Study Section
Special Emphasis Panel (ZHG1-HGR-N (O1))
Program Officer
Schloss, Jeffery
Project Start
2004-09-30
Project End
2007-09-30
Budget Start
2006-05-01
Budget End
2007-04-30
Support Year
3
Fiscal Year
2006
Total Cost
$575,851
Indirect Cost

  Institution

Name
Stanford University
Department
Biochemistry
Type
Schools of Medicine
DUNS #
009214214
City
Stanford
State
CA
Country
United States
Zip Code
94305

  Publications

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