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AIDS-Related Cancers

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Burkitt Lymphoma Genome Sequencing Project (BLGSP) Standard Operating Procedures (SOP) Manual

Burkitt Lymphoma Genome Sequencing Project (BLGSP): The Epstein-Barr Virus (EBV) Sequences from Burkitt Lymphoma Cases Published in Grande, Gerhard et al.,2019

The EBV sequences are available for download as BAM alignments from the Public directory at the DCC: https://cgci-data.nci.nih.gov/Public/BLGSP/WGS/L2/.  

The 106 BAM files made available by an open access are the Epstein-Barr virus (EBV) sequences that were extracted from the BLGSP patient cohort 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)

The following intentionally stringent criteria were used to ensure that no human reads were included in the BAMs.

  • Only reads aligned to the EBV genome (chrEBV) in the reference (GenBank accession AJ507799.2) were included. 
  • Unmapped reads were excluded. 
  • Reads whose mate did not align to the same chromosome (i.e. chrEBV) were excluded. 
  • Reads with more than 5 clipped bases (soft- or hard-clipped) in case of a split read (e.g. due to an EBV genome integration event) were excluded. 

As an additional check, the number of reads in EBV-negative tumors were counted with the expectation of finding virtually nothing if human reads are not contaminating. Out of 35 EBV-negative genomes, 25 (71%) had exactly zero reads. The remaining genomes, with one exception (which had 90), had at most 19 (range: 1-19) reads. When a few randomly selected reads were attempted to align to the human genome, only short matches (20-30 bp) were found that were expected to be spurious. Therefore, it is believed that these are real EBV reads.

Given that EBV is ubiquitous (e.g. over 90% of adults globally and most African children are infected), it is possible that EBV-infected normal B cells were included at very low levels in otherwise EBV-negative tumor biopsies. This would explain the presence of a few EBV reads found in EBV-negative BL samples. In general, EBV reads are often found in DNA sequencing data. For more information, see http://www.cureffi.org/2013/02/01/the-decoy-genome/ .Therefore, we are confident that there are virtually no human reads in these EBV BAM files, consistent with the strict criteria that were used.

Cancer Therapy Evaluation Program

The Cancer Therapy Evaluation Program (CTEP) seeks to improve the lives of cancer patients by finding better treatments, control mechanisms, and cures for cancer. CTEP funds a national program of cancer research, sponsoring clinical trials to evaluate new anti-cancer agents.

Experimental Methods for the Burkitt Lymphoma Genome Sequencing Project

On this page, researchers can find data generation and data analysis protocols from the following manuscript :

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)

Genomic Data Commons (GDC)

NCI's Genomic Data Commons (GDC) is a unified data sharing platform that allows users to search, browse, download, and analyze data. The GDC serves as a single knowledge base which unifies genomic and clinical data from different research programs for the cancer research community. 

Guide to Accessing Program Data

Visit the Guide to Accessing Data page for a visual and interactive guide on how to access OCG program data. 

HIV+ Tumor Molecular Characterization Project (HTMCP) Standard Operating Procedures (SOP) Manual

NCI’s Lung Cancer page

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