Novel Diagnostic Sequencing System for HIV Resistance Testing

DESCRIPTION (provided by applicant): 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. 0