We found a match
Your institution may have access to this item. Find your institution then sign in to continue.
- Title
Validation and calibration of next-generation sequencing to identify Epstein-Barr virus-positive gastric cancer in The Cancer Genome Atlas.
- Authors
Camargo, M.; Bowlby, Reanne; Chu, Andy; Pedamallu, Chandra; Thorsson, Vesteinn; Elmore, Sandra; Mungall, Andrew; Bass, Adam; Gulley, Margaret; Rabkin, Charles
- Abstract
The Epstein-Barr virus (EBV)-positive subtype of gastric adenocarcinoma is conventionally identified by in situ hybridization (ISH) for viral nucleic acids, but next-generation sequencing represents a potential alternative. We therefore determined normalized EBV read counts by whole-genome, whole-exome, mRNA and miRNA sequencing for 295 fresh-frozen gastric tumor samples. Formalin-fixed, paraffin-embedded tissue sections were retrieved for ISH confirmation of 13 high-EBV and 11 low-EBV cases. In pairwise comparisons, individual samples were either concordantly high or concordantly low by all genomic methods for which data were available. Empiric cutoffs of sequencing counts identified 26 (9 %) tumors as EBV positive. EBV positivity or negativity by molecular testing was confirmed by EBER-ISH in all but one tumor evaluated by both approaches (kappa = 0.91). EBV-positive gastric tumors can be accurately identified by quantifying viral sequences in genomic data. Simultaneous analyses of human and viral DNA, mRNA and miRNA could streamline tumor profiling for clinical care and research.
- Subjects
STOMACH cancer; CANCER diagnosis; NUCLEOTIDE sequencing; EPSTEIN-Barr virus diseases; DIAGNOSTIC use of in-situ hybridization; MESSENGER RNA; MICRORNA; VIRAL genes; ADENOCARCINOMA; DIAGNOSIS
- Publication
Gastric Cancer, 2016, Vol 19, Issue 2, p676
- ISSN
1436-3291
- Publication type
Article
- DOI
10.1007/s10120-015-0508-x