Informed consent was provided by all participants, and this study was selleck products approved by both the ethics committee of the Chinese University of Hong Kong and the Clinical Research Ethics Committee of Sun Yat-sen University. Other details and additional experimental procedures are provided in the Supplementary Materials and Methods. Whole-genome sequencing reads were mapped to both the human reference genome (UCSC hg19) and the EBV reference

genome (NC_007605). Whole-genome sequencing of the AGS–EBV and AGS cells showed a sequencing depth of 59-fold in AGS–EBV, and 42-fold in AGS for the human genome. A total of 91.59% and 91.57% of the whole genome region in AGS–EBV and AGS,

respectively, were covered with more than 10 reads. Moreover, an 897-fold sequencing depth covering 91.38% of the whole EBV genome was obtained in AGS–EBV cells only (Supplementary Figure 1A). Therefore, Ku-0059436 approximately 15 EBV episomes in 1 AGS–EBV cell could be inferred (897-fold EBV/59-fold human = 15.2), consistent with the findings by others. 11 In an attempt to uncover the EBV gene expression status in gastric cancer cells, 154.09 Mb reads of the AGS–EBV transcriptome were mapped to the EBV genome, with sequencing reads distributed across the entire EBV genome (Figure 1A). Visualization of transcriptome sequencing coverage across the EBV genome showed an EBV transcription profile in AGS–EBV cells with active regions similar to those identified in type I latency Burkitt’s lymphoma cells ( Supplementary Figure 1B). 12 Robust viral gene expression was yielded in AGS–EBV cells, with a median expression level of all not genes being 255.4 reads per kilobase per million (RPKM) ( Figure 1B). Transcriptome analysis of AGS–EBV identified the expression of 9 EBV genes (BARF0, BARF1, BcLF1, BHRF1, BLLF1, BRLF1, BZLF1, EBNA1, and LMP2A) previously detected in EBV(+) gastric tumors, and 71 EBV genes not reported previously in gastric cancer. The expression levels

of these 71 genes are higher than that of LMP2A (27.0 RPKM), which could be well validated by reverse-transcription (RT)-PCR ( Figure 1B and Supplementary Tables 1 and 2). The top 11 EBV genes (BNLF2a, BNLF2b, BHRF1, BFRF1, BFRF2, BFRF3, BKRF4, BMRF2, BKRF3, BMRF1, and BFRF1A) were verified in AGS–EBV and 2 other EBV(+) gastric cancer cell lines with natural EBV infection (SNU719 and YCCEL1) by RT-PCR. The expression of all 11 genes was detected in the 3 EBV(+) gastric cancer cell lines, but not in EBV(-) AGS cells ( Figure 1B). Notably, BHRF1, a viral oncogene detected in EBV(+) gastric cancer, 13 and 14 was the third most highly transcribed EBV gene in AGS–EBV (5103.9 RPKM).