A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers (RNA-Seq)

The incidence of HPV-related oropharyngeal squamous cell carcinoma (OPSCC) has increased more than 200% in the past 20 years. Recent genetic sequencing efforts have elucidated relevant genes in head and neck cancer, but HPV-related tumors have consistently shown few DNA mutations. In this study, we sought to analyze alternative splicing events (ASE) that could alter gene function independent of mutations. To identify ASE unique to HPV-related tumors, RNA sequencing was performed on 46 HPV-positive OPSCC and 25 normal tissue samples. A novel algorithm using outlier statistics on RNA-sequencing junction expression identified 109 splicing events, which were confirmed in a validation set from The Cancer Genome Atlas. RNA-sequencing data for 47 HPV+ HNSCC tumors, 25 normal UPPP, 2 HPV+ HNSCC patient derived xenografts, and 2 HPV+ HNSCC cell lines (SCC-090, SCC-047) ---------------------------------------------- Submitter declares that the raw data from patients will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.