Analysis of Epstein-Barr Virus in Pediatric Burkitt Lymphoma

Data Analysis Protocols
Data Analysis Protocol

The Epstein-Barr virus (EBV) sequences are available for download as BAM alignments from the public directory at the OCG Data Coordinating Center: These 106 open access EBV BAM files were extracted from the BLGSP patient genomes included in the following publication:

Grande BM, Gerhard DS, Jiang A, et al. Genome-wide discovery of somatic coding and non-coding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood. March 2019; 21;133(12):1313-1324. (PMID: 30617194)

Tumor EBV status and genome type 

Tumor EBV status and genome type was inferred from tumor whole genome sequencing (WGS) and RNA sequencing (RNA-seq) data. To determine tumor EBV status, the fraction of reads aligning to the EBV genome was calculated using Samtools (version 1.6). Tumors were considered to be EBV-positive when the EBV fraction of WGS reads was greater than 0.00006 (calculated from the fraction represented by the EBV genome in the reference genome) and the number of RNA-seq reads mapped to the EBER1 (chrEBV:6629-6795) and EBER2 (chrEBV:6956-7128) loci in the JAGuaR-based alignments was greater than 250. There were no cases with discordant EBV statuses inferred from the WGS and RNA-seq data. Although EBER expression was not quantified for the ICGC tumors because their RNA-seq data were not used in this project, they were all classified as EBV-negative according to their WGS data, which is consistent with the EBV status reported by the MMML-seq project. The minimum fraction of EBV reads was 0.01 for samples that underwent targeted sequencing to account for the different ratio of human and EBV genomic regions due to hybridization capture. EBV genome type was inferred for EBV-positive tumors by comparing the counts for 21-mers that are unique to either EBV type 1 (GenBank accession NC_007605.1) or type 2 (GenBank accession NC_009334.1). K-mer counting was performing on tumor WGS reads aligned to the EBV genome using Jellyfish (version 2.2.6). EBV genome type was inferred to be type 1 or type 2 if the count ratio of EBV type 1–specific k-mers to EBV type 2–specific k-mers was greater than or lesser than 1, respectively.

Last updated: June 15, 2020