Rapid DNA Assay System for Characterization of Infectious Disease Pathogens

DESCRIPTION (provided by applicant): We propose, using a high-sensitivity MagArray DNA detection system, to develop a rapid assay for infectious disease pathogens. In particular we will develop an assay for a large number of HPV genotypes using the MagArray platform. The viral origin of cervical cancer is now well established. Recent studies have shown that Human Papilloma Virus (HPV) DNA can be found in 99.7% of all cervical carcinomas. Because different HPV subtypes carry different risks for the development of cancer, a detection method that can distinguish subtypes could guide clinical care and offer new epidemiological insights. Current detection methods are limited to genotyping 30-35 of the more than 100 HPV types, and this is most often done by PCR. Detection, genotyping and analysis of broad spectrum of HPVs using a small amount of DNA that can be extracted from clinical samples would represent significant progress. Here we propose to adapt the MagArray platform to detect a broad spectrum (all types) of HPVs. The MagArray platform is based on using magnetic nanoparticles to tag the target fragments, rather than fluorescent molecules, as is the present practice. The advantage of using magnetic nanoparticles (typically 15 nm in diameter) as tags rather than fluorescent molecules is an enormous increase in sensitivity. With fluorescent labeling, one typically needs 100,000 fluorescently labeled molecules to obtain a signal/noise ratio adequate for reliable identification. MagArray technology will serve as a sensitive, specific diagnostic tool to detect multiple HPV types. In the first year feasibility studies will be performed for the high-risk genotypes HPV-16 and HPV-18 associated with cervical cancer. In the second year, we will determine the sensitivity and selectivity of at least 20 HPV types with a single sample, representing a large portion of the known types, most of which are strongly associated with anogenital and oral cancers. All these HPV types will be detected in a single experiment. This will reduce the cost, the time required for typing, and the amount of DNA sample required on a per-type basis. The application and development of MagArray technology to HPV-related cancer will serve as a basis for many applications in other infectious disease and cancer research and related clinical management. This technology has the potential to be integrated in a compact device that is simple and easy to use as a Point-of-Care system for molecular diagnostic applications.