DNA-Based Lateral Flow Assay for Oncogenic Strains of HPV

DESCRIPTION (provided by applicant): Human Papilloma Virus (HPV) comprises a family of viruses of over 100 different strains. The high-risk strains of HPV cause cervical cancer, which is the second leading cause of female cancer mortality worldwide with 288,000 deaths yearly. The goal of the proposed work is to develop a DNA-based diagnostic test for the oncogenic strains of HPV that is more rapid and has significantly lower false positives and false negatives than the currently available test. In Phase I, Trevigen established proof-of -principal for a combined real-time DNA amplifacation technique called LAMP (loop-mediated amplification) with cleavage by thermophilic DNA repair enzymes (SNIPases), of an immobilized probe targeted to the E7 gene of HPV16, an oncogenic strain that causes over 50% of all cervical cancers. The presence of the cleavage product, diagnostic for the HPV16 target DNA, was detected as a colored band on a lateral flow membrane. The lateral flow platform was chosen because of its simplicity and readout in less than 10 minutes. Under Phase II funding, we propose to optimize the real-time DNA amplification (PCR or LAMP) and the SNIPase cleavage reaction with a new hyperthermophilic AP endonuclease from Pyrobaculum aerophilum called PA-Endo IV, in a process known as PCR-SNIPase or LAMP-SNIPase, leading to a colored band on a dipstick within 1.5 hour from start to finish. The combination of the DNA amplification with the SNIPase reaction will reduce false positives and negatives because PA-Endo IV only cleaves the immobilized probes only when they are perfectly hybridized to their appropriate oncogenic HPV strain target DNA. The reaction will be multiplexed to allow detection and identification of all 13 oncogenic strains of HPV in four reactions using four radial lateral flow devices to be developed as part of this Phase II application. Finally, our optimized HPV test will be tested and qualified on archived cervical samples from a cohort of high-risk patients. The Phase II funding will lead to the development of a robust and rapid test for detection and identification of oncogenic strains of HPV that will significantly reduce the incidence of false positives and therefore reduce the need for colpsocopy, an expensive and invasive procedure. The simplicity of the assay will allow its implementation in a new efficacious "screen-and-treat" procedure for underserved populations.