Development And Validation Of A Capture Based Ngs Assay That Enables The Detection Of Epstein Barr Virus From Gastric Cancer Patients' Tumor Tissues

Background: Gastric cancer patients with positive test for Epstein Barr virus (EBV) in their tumors have been reported to benefit significantly from anti-PD-1 therapy. Current clinical testing relies on fluorescent in situ hybridization of EBV-encoded small RNA (EBER). NGS assays have been increasingly used in the clinical settings to make therapeutic recommendations to cancer patients due to its versatility in detecting various types of genomic alterations. Detecting EBV by NGS is highly desired. Method: DNA was extracted from the FFPE samples of 214 gastric cancer patients9 tumors, and profiled by the comprehensive NGS assay. A classification algorithm was developed using 131 gastric cancer samples (EBV Pos, n = 31; EBV Neg, n = 100) with known EBV status derived from EBER. The algorithm and the predetermined cutoff was then applied to an independent sample set (EBV Pos, n = 30; EBV Neg, n = 53) to evaluate the test performance. Results: In the training set, we achieved a sensitivity of 93.5% at a specificity of 100%. In the validation set, we achieved a sensitivity of 93.3% at a specificity of 100%. Using the same algorithm and cutoff, in the patients with tumor content above 20%, we achieve a sensitivity of 97.9% at a specificity of 100%. Conclusion: We developed a method to detect EBV in gastric tumors9 FFPE samples through a capture-based NGS assay. We also demonstrated strong concordance with an orthogonal assay (EBER) in detecting EBV. Citation Format: Yajie Hu, Bo Yang, Lei Wang, Shiyi Liu, Lei Liang, Jie Wang, Fugen Li, Yu Sun. Development and validation of a capture based NGS assay that enables the detection of Epstein Barr virus from gastric cancer patients9 tumor tissues [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 789.