SBIR-STTR Award

As of 2003 the CDC estimated that there were approximately 1.1 million persons in the U.S. infected with HIV- 1 and about 40,000 new cases are diagnosed each year. During the mid-to-late 1990s, advances in treatment slowed the progression of HIV to AIDS and related deaths. Unfortunately, the treatment often leads to the emergence of drug resistant mutants of HIV-1. The knowledge of the HIV-1 variants present in a patient is extremely important to effectively plan disease management. It is estimated that about 8% of HIV-1 infections in the US is caused by drug resistant HIV-1 variants and current guidelines recommend HIV-1 resistance genotyping before therapy and to monitor therapy effectiveness. However, current tests that rely on conventional DNA sequencing methods do not detect low-levels (<20%) of drug-resistant strains and therefore may not provide the necessary diagnostic information for effective treatments. The goal of this proposal is to develop a highly sensitive and cost-effective system for HIV-1 resistance genotyping (SBS-GEN) based on IBS' high-speed massively parallel DNA sequencing system. IBS' sequencing-by-synthesis system is based on the use of cleavable fluorescent nucleotides with reversible terminator technology. These features enable efficient removal of fluorescent signals and sequencing of repeats. During Phase I of this project, we will evaluate and optimize several critical parameters of the sequencing process using model systems. We will also conduct feasibility studies using cloned HIV-1 reverse transcriptase genes and build a prototype of the low cost HIV-1 genotyping instrument. During Phase II extensive validation of the prototype using validated clinical samples will be performed. Dr. Daniel Kuritzkes, an expert in the HIV-1 treatment and resistance will serve as a consultant for this project. Successful accomplishment of the Phase I milestones and completion of a subsequent Phase II validation will result in the development of an ultra-high throughput system which can be used for rapid, highly-sensitive and cost- effective HIV-1 resistance genotyping. 0 The proposed research is aimed at the development of a high-sensitivity sensitive, cost-effective HIV-1 resistance genotyping system which is powered by massively parallel DNA sequencing by synthesis (SBS). Compared to current technology based on DNA sequencing, the Intelligent Bio-Systems' approach will be able to rapidly detect low levels (1-20%) of multiple drug resistant HIV-1 variants in patient's plasma. The major application of the SBS-GEN HIV-1 genotyping product will be the detection of the presence, at levels 1-20%, of the viral population with drug-resistance. The SBS-GEN HIV-1 genotyping system will be used in patients undergoing anti-retroviral drug therapy to monitor its effectiveness, changing the treatment regimen, or patients newly diagnosed with HIV-1 infection.

As of 2003 the CDC estimated that there were approximately 1.1 million persons in the U.S. infected with HIV- 1 and about 40,000 new cases are diagnosed each year. During the mid-to-late 1990s, advances in treatment slowed the progression of HIV to AIDS and related deaths. Unfortunately, the treatment often leads to the emergence of drug resistant mutants of HIV-1. The knowledge of the HIV-1 variants present in a patient is extremely important to effectively plan disease management. It is estimated that about 8% of HIV-1 infections in the US is caused by drug resistant HIV-1 variants and current guidelines recommend HIV-1 resistance genotyping before therapy and to monitor therapy effectiveness. However, current tests that rely on conventional DNA sequencing methods do not detect low-levels (

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Thesaurus Terms:
Genotype Aids, Dna, Dna Directed Dna Polymerase, Haart (Highly Active Antiretroviral Therapy), Rna, Rna Directed Dna Polymerase, Alkyne, Azide, Base, Carbamate, Cell, Chemical Cleavage, Chemistry, Chemotherapy, Conditioning, Death, Density, Drug Resistance, Endopeptidase, Ether, Fluorescent Dye /Probe, Gene, Glass, Infection, Ionophore, Lead, Material, Model, Mutant, Nucleic Acid Sequence, Nucleotide, Optics, Performance, Plasma, Plasmid, Plastic, Reading, Temperature, Therapy, Transfection /Expression Vector