Abstract 5345: Somatic mutation status in cfDNA between therapy responders and non-responders of oropharyngeal squamous cell carcinoma patients

Abstract

Abstract Circulating tumor DNA (ctDNA) could potentially be utilized as a biomarker in Oropharyngeal Squamous Cell Carcinoma (SCC) patients. The objective of this study was to determine if somatic variants could be detected in circulating cell-free DNA (cfDNA) of Oropharyngeal SCC patients using Next Generation Sequencing (NGS). Somatic mutations have been reported in Orophayngeal SCC cases. The identification and detection of somatic variants in circulating cell-free DNA in patient's plasma may predict response to therapy, help monitor disease progression, guide therapy, and determine likelihood of recurrence. In this study, we compared the somatic mutation status between therapy responders and non-responders among Orophayngeal SCC patients. IRB approval was obtained and 23 Oropharyngeal SCC patients were identified in our patient database. Genomic DNA was isolated from frozen tumor tissue using NucleoSpin Tissue kit by Clontech. Cell-Free (cfDNA) was then extracted from patient's plasma samples using Zymo's Quick-cfDNATM serum and plasma kit. The quality and size of DNA was determined by Agilent 2200 TapeStation. If genomic DNA contamination was identified it was removed with Zymo Select-a-Size DNA kit. Libraries were prepared with 10 to 25 ηg of cfDNA using Accel-Amplicon 56G Oncology Panel of Swift Biosciences. DNA sequencing was then performed on MiSeq platform with Miseq Reagent Kit. Variants were identified using Biomedical Genomic Workbench and Genialis's online data analysis platform for Swift Biosciences's Accel-amplicon panels. From the 23 matched samples, 8 somatic non-synonymous variants were found in both tissue and plasma, 7 of which were present in non-responders. The variants and their allele frequencies in the non-responder group were as follows (tumor DNA /cfDNA in %) HRAS Gly12Cys (36.54/0.45), TP53 Glu298* (5.48/0.21), CDKN2A Pro114Arg (48.11/1.52), TP53 Arg282Trp (46.47/1.77), FBXW7 Arg505Gly (30.17/0.58), FBXW7 Arg505Leu (30.46/0.64), TP53 Arg273Cys (38.91/2.51), and one variant in the responder group PTEN (21.07/0.67) Arg130Gln. In conclusion, somatic non-synonymous variants can be identified in cfDNA from Oropharyngeal SCC patients using NGS. The number of detected variants is far greater in the non-responder group suggesting somatic variant detection could be a prognostic marker for Oropharyngeal SCC patients. Citation Format: Alok R. Khandelwal, Adam Greer, Rhett Orgeron, Mickie Hamiter, Xiaohui Ma, Tara Moore-Medlin, Hong Yin, Glenn Mills, Cherie-Ann O. Nathan. Somatic mutation status in cfDNA between therapy responders and non-responders of oropharyngeal squamous cell carcinoma patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5345.