A Novel genomics-based approach to differentiate HPV-positive and -negative HNC

描述（由申请人提供）：与HPV阴性OPSCC相比，HPV阳性OPSCC预后更好。其中一个挑战是引出哪些信号通路在HPV相关OPSCC的肿瘤发生中起关键作用。最近，外显子组测序已经鉴定出HNSCC中具有良好特征的体细胞突变，其可预测结果。尽管外显子组测序是鉴定驱动突变的流行工具，但它未能捕获基因表达变化的复杂性或鉴定可能更具治疗相关性的基因融合。最近，我们使用离子Torrent AmpliSeq面板分析进行DNA测序，以检测突变，并使用来自HPV阳性阴性疾病的OPSCC病例的福尔马林固定和石蜡包埋（FFPE）样本进行基因表达谱分析。我们的初步分析显示，HPV阳性和阴性样本之间的凋亡途径的显着区别的表达签名。基于我们的初步数据，我们假设RNA-Seq是一种基于基因组学的方法，在识别HPV阳性和阴性OPSCC中的治疗可行突变和基因表达特征方面上级外显子组seq，因此可以更好地帮助优化OPSCC患者的治疗。因此，我们也有兴趣使用来自我们口咽数据库的存档FFPE样本将这些特征和突变与临床变量相关联。这项研究将使OPSCC患者更好地分层，并更好地了解这种疾病的生物学。因此，我们的研究具有高度转化性，可能会影响未来的患者护理。两个具体目标将帮助我们实现目标。Specific Aim 1将优化组合RNA-seq和WES方法，用于使用从我们的OPSCC数据库中选择的30个存档FFPE样本识别HPV阳性与HPV阴性OPSCC中的可操作突变和基因表达特征。具体目标2将建立一个强大而有效的工作流程，以确认OPSCC中的突变，拷贝数异常和差异基因表达，并将区分HPV阳性和阴性OPSCC中基因表达特征和驱动突变的患病率，并使用我们的数据库将这些与临床变量相关联。

DESCRIPTION (provided by applicant): HPV positive OPSCC carries a better prognosis compared to HPV negative OPSCC. One of the challenges is to elicit which signaling pathways play a key role in tumorigenesis of HPV related OPSCC. Recently, exome sequencing has identified well characterized somatic mutations in HNSCC that are predictive of outcome. Despite it being a popular tool for identifying driver mutations, exome sequencing fails to capture the complexity of changes in gene expression or identifying gene fusions that may be more therapeutically relevant. Recently, we performed DNA sequencing using ion Torrent AmpliSeq panel analysis to detect mutations and a nano Striping's cancer reference panel for gene expression profiling using formalin fixed and paraffin embedded (FFPE) samples from OPSCC cases with HPV-positive negative disease. Our preliminary analysis revealed significant distinguished expression signatures in apoptosis pathway between the HPV positive and negative samples. Based on our preliminary data, we hypothesize that RNA-Seq, a genomics based approach, is superior to exome seq for identifying therapeutically actionable mutations and gene expression signatures in HPV-positive and negative OPSCC and can therefore better help optimizing therapy for patients with OPSCC. We are therefore interested as well in correlating these signatures and mutations with clinical variables using archival FFPE samples from our oropharyngeal database. This study will allow a better stratification of patients with OPSCC and better understanding of the biology of this disease. Therefore, our studies are highly translational and could impact future patient care. Two specific aims will help us achieve our goals. Specific Aim1 will optimize a combined RNA-seq and WES approach for identifying actionable mutations and gene expression signatures in HPV-positive versus HPV-negative OPSCC using 30 archival FFPE samples selected from our OPSCC database. Specific Aim 2 will build a robust and efficient workflow to confirm mutations, copy number abnormalities and differential gene expression in OPSCC and will differentiate the prevalence of gene expression signatures and driver mutations in HPV-positive and negative OPSCC and correlate these with clinical variables using our database.