Developing a POC CMOS biochip for oral HPV detection and quantification

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 DESCRIPTION (provided by applicant): Human Papilloma Virus (HPV) oral infection is responsible for an increasing percent of head and neck cancers. The risk of progression from infection to cancer is increased by persistent HPV infection, infection with high-risk HPV types, high viral load and increased abundance of HPV E6/E7 transcripts and host p16INK4A transcripts. Rapid cost-effective point- of-care (POC) tests that detect and quantify risk-associated biomarkers in oral biospecimens are needed for oral cancer screening, prognostic purposes and to follow-up persons treated for high-grade lesions. Hypothesis: We hypothesis that it is possible to use the InSilixa HYDRA-1K CMOS biochip to develop a multiplex assay that can detect, identify and quantify HPV high and low risk types in oral tissues and fluids. Preliminary Data: Co-investigators at UNC have developed a non POC multiplex qPCR assay that can detect, identify and quantify HPV 6, 11, 16 and 18 L1 gene type-specific sequences and HPV E1 gene consensus sequences common to all HPV types. This assay has been used in clinical studies of oral biosamples. InSilixa engineers have developed the 1,024 sensor pixel multiplex HYDRA-1K CMOS biochip and used this platform to identify 117 separate SNPs in the M. tuberculosis genome that confer drug resistance. Specific Aims: The proposed Phase I project seeks to develop a complementary metal-oxide-semiconductor (CMOS) platform, the InSilixa HYDRA-1K, as a POC molecular diagnostic device that can detect, type and quantify HPV DNA in oral biospecimens. In Specific Aim 1 we will design, fabricate, test and optimize HPV type-specific and generic capture probes attached to a dynamic microarray experimental setup and proxy for the InSilixa HYDRA-1K biochip. In Specific Aim 2 we will design, fabricate, test and optimize primers for an asymmetric quantitative multiplex PCR assay that amplifies regions of the HPV genome that contain HPV type-specific and consensus sequences. In Specific Aim 3 we will determine the performance specifications of a HPV dynamic microarray assay that integrates the capture probes from Specific Aim 1 with the asymmetric quantitative multiplex PCR assay from Specific Aim 2. Successful completion of these Specific Aims will provide the basis for a Phase II SBIR application that will migrate the HPV assay developed here from the dynamic microarray setup to the HYDRA-1K CMOS platform.