title: Validation and calibration of next-generation sequencing to identify Epstein-Barr virus-positive gastric cancer in The Cancer Genome Atlas.
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.
authors.affiliation: Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA.
authors.forename: M Constanza
authors.initials: MC
authors.lastname: Camargo
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
authors.forename: Reanne
authors.initials: R
authors.lastname: Bowlby
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
authors.forename: Andy
authors.initials: A
authors.lastname: Chu
authors.affiliation: The Eli and Edythe L. Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02142, USA.|Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
authors.forename: Chandra Sekhar
authors.initials: CS
authors.lastname: Pedamallu
authors.affiliation: Institute for Systems Biology, Seattle, WA, 98109, USA.
authors.forename: Vesteinn
authors.initials: V
authors.lastname: Thorsson
authors.affiliation: Department of Pathology and Laboratory Medicine and the Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
authors.forename: Sandra
authors.initials: S
authors.lastname: Elmore
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Mungall
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
authors.forename: Adam J
authors.initials: AJ
authors.lastname: Bass
authors.affiliation: Department of Pathology and Laboratory Medicine and the Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
authors.forename: Margaret L
authors.initials: ML
authors.lastname: Gulley
authors.affiliation: Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA. rabkinc@mail.nih.gov.
authors.forename: Charles S
authors.initials: CS
authors.lastname: Rabkin
mesh_terms: D002138:Calibration; D020031:Epstein-Barr Virus Infections / Q000150:complications* / Q000235:genetics; D015894:Genome, Human; D004854:Herpesvirus 4, Human / Q000472:pathogenicity; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D035683:MicroRNAs; D016612:Paraffin Embedding; D013274:Stomach Neoplasms / Q000235:genetics / Q000821:virology*
chemical_list: D035683:MicroRNAs
keywords: EBV; Molecular subtypes; Stomach cancer; TCGA