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Nuclease Probe Mediated Sequencing

Award Information

Department of Health and Human Services
Award ID:
Program Year/Program:
2010 / SBIR
Agency Tracking Number:
Solicitation Year:
Solicitation Topic Code:
Solicitation Number:
Small Business Information
3430 E. Global Loop TUCSON, AZ 85706-
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Woman-Owned: No
Minority-Owned: No
HUBZone-Owned: No
Phase 1
Fiscal Year: 2010
Title: Nuclease Probe Mediated Sequencing
Agency: HHS
Contract: 1R43HG005949-01
Award Amount: $599,268.00


DESCRIPTION (provided by applicant): Sequencing is very powerful for identifying differences in genomic DNA that may regulate cell function and diseases, pre-dispose persons to certain diseases, or warn of adverse drug metabolism. It provides a basis for i dentifying differences in gene expression, though such applications have been limited and are problematic because each expressed gene can vary from a single copy per cell to 10's of thousands of copies. Further, its application to formalin fixed paraffin-e mbedded tissue (FFPE) is quite challenging. Millions of such samples, along with the corresponding treatment modalities and known clinical outcomes, are archived at clinical centers and hospitals. Millions of such samples have also been archived from in vi vo studies of safety, metabolism, and animal models of disease. In addition, the utility of sequencing for routine experiments where array-based measurements are used today is limited by cost, and might also be limited by accuracy, sensitivity, and reprodu cibility of the sequencing data. This Phase I proposal develops and validates a new approach for addressing these challenges, Nuclease Probe Mediated Sequencing, provides a variation of candidate capture methods used to focus sequencing onto genes of int erest, and addresses issues with array-based methods. The method proposed uses a lysis-only assay and either a variation of HTG's quantitative Nuclease Protection Assay (qNPA ) or ligation/exonuclease generated Padlock probes to generate DNA probes for seq uencing by synthesis, combined with gene tagging and experiment tagging methods to permit pooling to provide cost reduction and higher sample throughput. PUBLIC HEALTH RELEVANCE: This Phase I project will address challenges to using sequencing for m easuring gene expression. The proposed method will enable researchers to use archived fixed tissue samples. It will also lower the cost per sample and increase the number of samples tested per sequencing run, while potentially increasing the accuracy, dyna mic range and reproducibility of measurement, expanding the utility of sequencing to measure gene expression and providing a more cost effective and precise platform than currently provided by high density array-based measurement.

Principal Investigator:

Bruce E. Seligmann

Business Contact:
Small Business Information at Submission:

3430 E. Global Loop TUCSON, AZ -

EIN/Tax ID: 186091229
Number of Employees: N/A
Woman-Owned: No
Minority-Owned: No
HUBZone-Owned: No