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

Julius Honecker1, Dirk Paffenholz1, Julian Jungmann1

  • 1Foundation Medicine GmbH, Penzberg, Germany.

The Journal of Molecular Diagnostics : JMD
|July 25, 2025
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Summary

FoundationOne CDx and Heme assays accurately detect Epstein-Barr virus (EBV) in tumors, offering a reliable alternative to traditional methods for EBV-associated cancers.

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Area of Science:

  • Oncology
  • Virology
  • Genomics

Background:

  • Accurate Epstein-Barr virus (EBV) detection is crucial for diagnosing and managing EBV-associated cancers.
  • Conventional methods like EBER ISH can be time-consuming and may miss EBV presence in certain tumor types.

Purpose of the Study:

  • To validate the performance of FoundationOne CDx (F1CDx) and FoundationOne Heme (F1H) next-generation sequencing assays for EBV detection.
  • To compare the accuracy of these assays against the established EBER in situ hybridization (ISH) reference standard.

Main Methods:

  • A total of 413 tumor samples (gastric carcinoma, squamous cell carcinoma, diffuse large B-cell lymphoma) were analyzed.
  • Next-generation sequencing assays (F1CDx, F1H) were used to detect EBV, with results compared to EBER ISH.
  • Dilution experiments were conducted to assess assay linearity and dynamic range.

Main Results:

  • The F1CDx and F1H assays demonstrated high sensitivity (94.0%), specificity (99.1%), and accuracy (98.3%) for EBV detection.
  • Strong concordance with EBER ISH was observed (AUC = 0.97), with excellent precision (95.5%) and reproducibility (CV = 4.7%).
  • Linearity was confirmed across a broad dynamic range, and characteristic genomic alterations were associated with EBV-positive samples.

Conclusions:

  • F1CDx and F1H provide a reliable, parallel approach for detecting EBV alongside somatic genomic alterations in a single assay.
  • These assays offer a promising alternative to conventional ISH, potentially streamlining diagnostic workflows for EBV-related malignancies.
  • The method enhances the identification of EBV in tumors, even without initial clinical suspicion, aiding in diagnosis and management.