FoundationOne CDx and FoundationOne Heme Detect Epstein-Barr Virus with High Sensitivity and Specificity.

Accurate detection of Epstein-Barr virus (EBV) in tumors is essential for refining diagnosis and guiding management of EBV-associated cancers. This validation study evaluated the performance of the FoundationOne CDx (F1CDx) and FoundationOne Heme (F1H) next-generation sequencing assays for detecting EBV compared with the reference standard EBV-encoded RNA (EBER) in situ hybridization (ISH). A total of 413 samples of gastric carcinoma, squamous cell carcinoma (predominantly nasopharyngeal carcinoma), and diffuse large B-cell lymphoma was assessed. The assays demonstrated a sensitivity of 94.0%, specificity of 99.1%, and accuracy of 98.3% with an area under the curve of 0.97 for EBV detection, showing high concordance with EBER ISH. Precision was 95.5%, and reproducibility across multiple runs was strong (CV = 4.7%). Dilution experiments demonstrated a linear relationship between EBV viral reads per million and the degree of cell culture dilution (Pearson's R > 0.99, P < 0.001), supporting assay linearity over a broad dynamic range. Characteristic mutational and cytogenetic profiles, including losses at 9p21 and gains at 11q13, were observed in EBV-positive samples, supporting the clinical utility of the method. These results indicate that F1CDx and F1H provide a reliable, in-parallel approach for detecting EBV along with somatic genomic alterations in a single assay. This method offers a promising alternative to conventional ISH, especially for identifying EBV in tumors without initial clinical suspicion, potentially streamlining diagnostic workflows.