Clinical Application of Liquid Biopsy and Mate Pair Next Generation Sequencing for Oropharyngeal Cancer Patients

Oropharyngeal Cancer Patients Sarah Clark Biochemistry, Biology, Chemistry Background: Circulating tumor DNA (ctDNA) can be distinguished from other cell-free DNA in the body due to its unique mutations. Next generation sequencing and digital PCR have allowed detection of ctDNA to become a more commonly used tool, and because it can be detected directly out of blood, is called the liquid biopsy. Liquid biopsy has the ability to monitor cancer in real time. Mate pair sequencing minimizes the amount of sequencing needed to find the unique cancer-specific DNA breakpoints necessary for liquid biopsy. This research aims to investigate the clinical use of mate pair next generation sequencing and liquid biopsy in oropharyngeal squamous cell carcinomas (OPSCCs). Methods: Mate pair next generation sequencing (10 gigabases per sample) was used to find unique tumor DNA breakpoints. Sanger sequencing was then used to validate these junctions. This was followed by RTPCR to test the primers and fluorescent probes before running the samples on the RainDance digital droplet PCR platform. Results: Using sanger sequencing, we were able to validate 16 out of 18 of the junctions detected by mate pair next generation sequencing. We are now testing these validated primers to detect ctDNA corresponding to these tumors. Future: Liquid biopsy has the potential to greatly impact the clinical treatment of OPSCC. The use of mate pair sequencing, rather than traditional whole genome sequencing, could accelerate the acceptance of liquid biopsy into clinical practice.