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DNA Detection Switch (DDS) probes for diagnosis of multi-drug resistant…

Award Information

Agency:
Department of Health and Human Services
Branch:
N/A
Award ID:
95795
Program Year/Program:
2010 / SBIR
Agency Tracking Number:
AI090852
Solicitation Year:
N/A
Solicitation Topic Code:
NIAID
Solicitation Number:
N/A
Small Business Information
GENETAG TECHNOLOGY, INC.
GENETAG TECHNOLOGY, INC. 2421 Kings Arms Drive ATLANTA, GA -
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Woman-Owned: No
Minority-Owned: No
HUBZone-Owned: No
 
Phase 1
Fiscal Year: 2010
Title: DNA Detection Switch (DDS) probes for diagnosis of multi-drug resistant tuberculo
Agency: HHS
Contract: 1R43AI090852-01
Award Amount: $913,399.00
 

Abstract:

DESCRIPTION (provided by applicant): DDS diagnostic probe systems for MDR-TB Principal Investigator, Shafer, David A. PhD Abstract: Tuberculosis (TB) is a primary cause of morbidity and mortality in many areas of the world with about 8 million new cases an d 2 million deaths per year. In recent years, there has been a rapid and alarming increase in the incidence and spread of drug resistant TB and the frequency of multi-drug resistant TB (MDR-TB) is increasing worldwide. With most new cases arising from non- compliance or inappropriate treatment of drug susceptible TB, there is a serious need for rapid and precise diagnosis, particularly in the low-resource settings where TB and MDR-TB are prevalent. This translational grant is developing a set of molecular di agnostic probes for MDR-TB based upon new dual-component error-preventing probe technologies that were invented previously by the PI and that enable precise, clear-cut and reliable discrimination of single base mutants associated with resistance. These pro bes are suitable for end-point and array detection as well as real-time PCR (qPCR). Compared to standard probes for qPCR, these DDS (DNA Detection Switch) probes provide equivalent detection over a wide range of annealing/hybridization temperatures and the y can selectively detect a single base mutant and exclude detection of alternate variants at the same site. The program will focus on the design and testing of a comprehensive set of such DDS probes for qPCR that can detect the primary mutants in the rpoB gene that confer Rifampin (RIF) resistance and the key mutant sites in katG and inhA that confer Isoniazid (INH) resistance. Preliminary studies reported here demonstrate we have already achieved absolute single base discrimination with important katG and inhA mutants. We have also demonstrated an additional primer-based probe system called G-Force probes that can be used in conjunction with the internal DDS probes to thereby count the mutant vs. amplicon frequency - a new diagnostic capacity. Initial testi ng will be done with synthetic genes constructed with the major drug resistant variants. Further testing and blind studies will be conducted with DNA samples from well-characterized clinical isolates and pan- susceptible controls that are being provided by our colleagues at the CDC. The proposed DDS probes for MDR-TB can supplant standard Taqman or Molecular Beacon probes for qPCR that are costly, require careful optimization and are prone to false positives. Our DDS probes are also expected to improve upon the line probe assays of Hain and Innogenetics that typically provide shades of gray vs. absolute single base discrimination and that are frequently ineffective with smear negative samples or HIV co-infected patients. We have also outlined a series of pot ential secondary diagnostic products for MDR-TB that will follow and build on this Phase I program by translating these new probes to a simple chip format, to new research/diagnostic tools, and to a low-cost, hand- held end-point reader that we have alread y prototyped and that overcomes the need for real-time PCR instruments. The completion of these short and long range goals should provide valuable new tools for high end research and diagnostics and for clinical management in low resource settings. DDS dia gnostic probe systems for MDR-TB Principal Investigator, Shafer, David A. PhD Narrative: This grant is developing novel diagnostic probes for real-time PCR detection of multi-drug resistant tuberculosis (MDR-TB). The development program combines a proven n ucleic acid amplification platform with new dual-component error-preventing probe technologies called DDS (DNA detection switch) probes that were invented by the PI and that enable highly precise, clear-cut and reliable discrimination of single base mutant s over a wide range of annealing/hybridization temperatures. Standard probes do not provide such absolute single base discrimination and they require narrow temperature control. The program will focus on the design and testing of a comprehensive set of iDD S (internal DDS) probes that can detect the primary mutant sites in the rpoB gene that confer Rifampin (RIF) resistance and key mutant sites in the katG gene and the inhA promoter region that confer resistance to Isoniazid (INH). (RIF and INH are the first line drugs for TB control.) This technology can supplant standard Taqman probes for qPCR which are costly, require careful optimization and are prone to false positives, and it improves upon the line probe assays of Hain and Innogenetics that provide shad es of gray vs. absolute single base discrimination and that are frequently ineffective with smear negative samples or HIV co-infected patients. These diagnostic probes are intended for commercial distribution in hospital and clinical labs for testing and m onitoring infectious disease and for managing treatment.

Principal Investigator:

David A. Shafer
4046395479
DAVID.SHAFER@COMCAST.NET

Business Contact:

David Shafer
david.shafer@comcast.net
Small Business Information at Submission:

GENETAG TECHNOLOGY, INC.
GENETAG TECHNOLOGY, INC. 2421 Kings Arms Drive ATLANTA, GA -

EIN/Tax ID: 158255345
DUNS: N/A
Number of Employees: N/A
Woman-Owned: No
Minority-Owned: No
HUBZone-Owned: No