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Project Brief


Open Competition 3 - Biotechnology

High Throughput, Low Cost SNP Genotyping for Diagnostics and Genome Scanning


Develop a method for accurate simultaneous detection of up to 100,000 single nucleotide polymorphisms, or point mutations, in patient DNA, enabling rapid, low-cost genotyping, for disease diagnosis, susceptibility testing, and personalized medicine.

Sponsor: Gene Check, Inc.

1629 Blue Spruce Dr.
Suite 106
Ft. Collins, CO 80524
  • Project Performance Period: 10/1/2003 - 9/30/2006
  • Total project (est.): $1,915,468.00
  • Requested ATP funds: $1,762,178.00

The explosion of genetic information arising from the sequencing of human genomes provides unparalleled opportunities for advances in medical care. Single nucleotide polymorphisms (SNPs)--mutations affecting the pair of molecules forming a single "rung" of the double-helix DNA "ladder"--account for the vast majority of the 10 million sequence differences between any two humans. The ability to detect and genotype these SNPs may allow the mapping of disease genes, diagnosis of diseases, determination of predispositions to disease, and prediction of drug effects. In this three-year project, Gene Check will develop a rapid, low-cost method for accurately detecting and genotyping up to 100,000 SNPs in a single DNA sample. The method combines two extremely accurate and widely used processes: the homology searching ability of the bacterial recombination protein RecA and genotyping using oligonucleotide ligation assays (OLAs). The objective of this three-year project is to develop an RecA-OLA method that genotypes more than 20 SNPs per second in a fully automated system at a cost of less than $0.02 per SNP. A set of 100,000 SNPs could then be completely genotyped for less than $2,000 in less than three hours using off-the-shelf-instrumentation. The highest technical risk is that RecA proteins might interfere with DNA structure in a way that prevents the OLA process from working. Gene Check, a small company, earns insufficient profit to fund major research projects. The high risk inherent in this research makes potential investors and corporate partners unwilling to provide financing. ATP funding will allow Gene Check to undertake this project. If successful, this innovative method would bring immediate improvements to genomics, diagnostics, and health care. High-throughput, low-cost genotyping would hasten the mapping of genes associated with disease susceptibility along with predictive toxicities and efficacies of particular drugs in patients (pharmacogenomics). DNA analysis could be accomplished in hours, and affordable genetic profiling of patients could reduce hospitalization costs from adverse drug reactions by $1-4 billion. Furthermore, this new method would advance the discovery of highly effective gene therapies.

For project information:
Dr. Robert E. Wagner, (970) 472-9951
rwagner@genecheck.com

ATP Project Manager
Lawrence Uhteg, (301) 975-8779
lawrence.uhteg@nist.gov


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