Abstract

Next Generation Sequencing for the Clinical Management of Patients with Oropharyngeal Squamous Cell Carcinoma

David Smith, Professor, Mayo Clinic

There have been dramatic increases in the incidence of oropharyngeal squamous cell carcinoma (OPSCC) over the past several decades in the United States. This has been caused by an increased proportion of these cancers that contain human papillomavirus (HPV) due to changing sexual practices. The model for how HPV causes cancer is based upon our understanding of the role this virus plays in cervical cancer. In cervical cancer long term HPV infection ultimately results in integration of HPV into the human genome which causes genomic instability that eventually leads to invasive cervical cancer. However in OPSCC the situation is more complex. First, many patients have a history of smoking and drinking. In addition, all HPV positive OPSCCs are not the same, as some have very low expression of HPV transcripts and others have much more robust expression. We have been using mate-pair sequencing of DNA and RNAseq from OPSCC patients and have discovered that HPV integration is not as common in OPSCC as it is in cervical cancer. Our results analyzing both of these datasets reveals that valuable clinical information can be obtained on each OPSCC using both genome sequencing and RNAseq and suggest a new model for the clinical management of these patients.