Detection of viral pathogens in high grade gliomas from unmapped next-generation sequencing data.
Viral pathogens have been implicated in the development of certain cancers including human papillomavirus (HPV) in squamous cell carcinoma and Epstein-Barr virus (EBV) in Burkitt's lymphoma. The significance of viral pathogens in brain tumors is controversial, and human cytomegalovirus (HCMV) has been associated with glioblastoma (GBM) in some but not all studies, making the role of HCMV unclear. In this study we sought to determine if viral pathogen sequences could be identified in an unbiased manner from previously discarded, unmapped, non-human, next-generation sequencing (NGS) reads obtained from targeted oncology, panel-based sequencing of high grade gliomas (HGGs), including GBMs. Twenty one sequential HGG cases were analyzed by a targeted NGS clinical oncology panel containing 151 genes using DNA obtained from formalin-fixed, paraffin-embedded (FFPE) tissue. Sequencing reads that did not map to the human genome (average of 38,000 non-human reads/case (1.9%)) were filtered and low quality reads removed. Extracted high quality reads were then sequentially aligned to the National Center for Biotechnology Information (NCBI) non-redundant nucleotide (nt and nr) databases. Aligned reads were classified based on NCBI taxonomy database and all eukaryotic viral sequences were further classified into viral families. Two viral sequences (both herpesviruses), EBV and Roseolovirus were detected in 5/21 (24%) cases and in 1/21 (5%) cases, respectively. None of the cases had detectable HCMV. Of the five HGG cases with detectable EBV DNA, four had additional material for EBV in situ hybridization (ISH), all of which were negative for expressed viral sequence. Overall, a similar discovery approach using unmapped non-human NGS reads could be used to discover viral sequences in other cancer types.
Division of Neuropathology, Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States.
Patrick J
PJ
Cimino
Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States.
Guoyan
G
Zhao
Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, United States; Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States.
David
D
Wang
Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States.
Jennifer K
JK
Sehn
Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States; Department of Otolaryngology Head and Neck Surgery, Washington University School of Medicine, Saint Louis, MO, United States.
James S
JS
Lewis
Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States. Electronic address: EDuncavage@path.wustl.edu.
Eric J
EJ
Duncavage
D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002051:Burkitt Lymphoma / Q000821:virology; D002294:Carcinoma, Squamous Cell / Q000821:virology; D002648:Child; D056915:DNA Copy Number Variations; D005260:Female; D005910:Glioma / Q000175:diagnosis* / Q000821:virology*; D004854:Herpesvirus 4, Human / Q000302:isolation & purification; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007150:Immunohistochemistry; D008297:Male; D008875:Middle Aged; D027383:Papillomaviridae / Q000302:isolation & purification; D012367:RNA, Viral / Q000235:genetics / Q000302:isolation & purification*; D019211:Roseolovirus / Q000302:isolation & purification; D017422:Sequence Analysis, DNA
D012367:RNA, Viral
Glioblastoma; Gliosarcoma; Merkel cell; Next generation sequencing; Squamous cell carcinoma; Virus