Oropharyngeal squamous cell carcinoma (OPSCC) is a cancer of the base of the tongue and tonsils. This cancer was previously found in individuals with a smoking and drinking history but is increasingly being promoted by the presence of high risk types of human papillomavirus (HPV). In an attempt to determine the exact role that HPV plays in the development of this cancer we have been using mate-pair next generation sequencing (MP-Seq). Using MP-Seq we have found that HPV is only integrated into the human genome in 30% of HPV-positive OPSCCs, which is dramatically different than what is found in cervical cancer. MP-Seq not only can determine the physical status of HPV in a given sample, but can also ascertain genome-wide changes in any cancer. We describe how MP-Seq could be used in the clinical management of HPV-positive OPSCC patients. We have also explored another whole genome sequencing strategy that has been developed by the Beijing Genomics Institute. They can currently do whole genome sequencing for a total cost (and this includes analysis) of $600 and are developing methodologies to reduce this to $100. I will describe how these types of whole genome sequencing strategies could be used to direct therapies for these patients including facilitating the use of the liquid biopsy to monitor patients during their clinical treatment.
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