Abstract

Mate-Pair Next Generation Sequencing as a Powerful Clinical Tool for Monitoring Cancer Patients

David Smith, Professor, Mayo Clinic

Our laboratory studies oropharyngeal squamous cell carcinoma as it is cancer that is being increasingly driven by human papillomavirus. A powerful tool to characterize the physical status of HPV in any oropharyngeal carcinoma is mate-pair library construction followed by next generation sequencing (MP-Seq). We have done this and determined that HPV is only integrated into 30% of these cancers, thus most of these HPV-infected cancers develop just in the presence of episomal copies of HPV. The MP-Seq also reveals genome wide changes that have occurred in each of these cancers and in each we’ve identified multiple novel cancer-specific breakpoints. These can be used as molecular markers for monitoring the concentration of circulating free tumor DNA in the blood from these patients with another powerful technology, digital droplet PCR. We will describe our work testing the power of MP-Seq to aid in the clinical management of oropharyngeal squamous cell carcinoma patients at the Mayo Clinic.