The inventors have developed a highly sensitive and specific method for improved Human Papilloma Virus (HPV)-diagnostics, which defines the persistence of infection from which cancer risk can be drawn. The method involves a short protocol in the lab, sequencing technology and an algorithm that identifies HPV status and the cancer risk to guide clinical follow-up. The method will be a quicker and more clinically specific HPV test than those in the market today and can improve health alone or in combination with cytology. Intervention algorithms are today very complex and due to suboptimal clinical specificity, current strategies are elaborate, costly and highly time-consuming leaving women waiting for longer periods in insecurity.
This new strategy involves first of all a whole-genome sequencing of the HPV-genome to define the type of viruses that are involved. The researchers have developed an efficient protocol in lab, which includes sequencing of the complete HPV genome and segments of the human genome defining if the virus types have been integrated in the human DNA. These results classify the different cancer-risking types and will also grade the infection, labeling the duration of the infection. This again gives a more precise diagnose of a treatment-requirement since the grade of integration relieves the complexity of the virus attack and the need of a cancer treatment. All these analysis are made possible by a specialized and unpublished bioinformatic pipeline developed by the researchers. In addition have they simplified and optimized the sequencing protocol in a way that all that is needed to sequence up to 1500 samples in parallel only require a 2- or 3-step protocol. The prototype is today run at an Illumina platform, but can easily be transformed to any of the other leading platforms. Today they have a prototype of HPV16, the most carcinogenic and prevalent type, and they intend to include the remaining 6 high risk HPV types. These 7 virus types can all be included in an optimized lab-protocol that analyze up to 1500 samples in parallel. The entire protocol has been tested on different material including urine and liquid based cytology. The technology has been developed based on one cohort of Norwegian. We plan to provide further clinical validation, both on biobanked and prospectively collected clinical samples, for both the pre-diagnostic and monitoring setting.
A provisional patent application will be filed within 2016. The patent application will cover the primer sites and the specialized bioinformatic pipeline and claim diagnostic, prognostic and predictive use of the technology.