Absence of cytomegalovirus in high-coverage DNA sequencing of human glioblastoma multiforme

International Journal of Cancer

Volumn 136, Issue 4, 2015, Pages 977-981

  Tang, Ka Wei ^a   Hellstrand, Kristoffer ^b   Larsson, Erik ^a  

^a UNIVERSITY OF GOTHENBURG   (Sweden)

^b UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

Computational biology; Cytomegalovirus; Glioblastoma multiforme

Indexed keywords

VIRUS DNA;

ADULT; AGED; ARTICLE; CLINICAL ARTICLE; CONTROLLED STUDY; CYTOMEGALOVIRUS; DNA SEQUENCE; FEMALE; GENETIC VARIABILITY; GENOME ANALYSIS; GENOME SIZE; GLIOBLASTOMA; HUMAN; HUMAN TISSUE; MALE; MIDDLE AGED; NONHUMAN; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS; STRAIN IDENTIFICATION; VERY ELDERLY; VIRUS DETECTION; VIRUS GENOME; VIRUS LOAD; VIRUS STRAIN; YOUNG ADULT; BRAIN TUMOR; CYTOMEGALOVIRUS INFECTION; GENETICS; HIGH THROUGHPUT SEQUENCING; VIROLOGY;

ADULT; AGED; BASE SEQUENCE; BRAIN NEOPLASMS; CYTOMEGALOVIRUS; CYTOMEGALOVIRUS INFECTIONS; DNA, VIRAL; FEMALE; GLIOBLASTOMA; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; MIDDLE AGED; SEQUENCE ANALYSIS, DNA; YOUNG ADULT;

EID: 84918804391     PISSN: 00207136     EISSN: 10970215     Source Type: Journal    
DOI: 10.1002/ijc.29042     Document Type: Article

References (19)

1. Dziurzynski K, Chang SM, Heimberger AB, et al. Consensus on the role of human cytomegalovirus in glioblastoma. Neuro Oncol 2012;14:246-55
2. Cobbs CS, Harkins L, Samanta M, et al. Human cytomegalovirus infection and expression in human malignant glioma. Cancer Res 2002;62:3347-50
3. Bhattacharjee B, Renzette N, Kowalik TF. Genetic analysis of cytomegalovirus in malignant gliomas. J Virol 2012;86:6815-24
4. Ranganathan P, Clark PA, Kuo JS, et al. Significant association of multiple human cytomegalovirus genomic Loci with glioblastoma multiforme samples. J Virol 2012;86:854-64
5. Rahbar A, Orrego A, Peredo I, et al. Human cytomegalovirus infection levels in glioblastoma multiforme are of prognostic value for survival. J Clin Virol 2013;57:36-42
6. Soderberg-Naucler C. Treatment of cytomegalovirus infections beyond acute disease to improve human health. Expert Rev Anti-Infect Ther 2014; 12:211-22
7. Poltermann S, Schlehofer B, Steindorf K, et al. Lack of association of herpesviruses with brain tumors. J. Neurovirol 2006;12:90-9
8. Yamashita Y, Ito Y, Isomura H, et al. Lack of presence of the human cytomegalovirus in human glioblastoma. Mod Pathol, in press
9. Feng H, Shuda M, Chang Y, et al. Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 2008;319:1096-100
10. Khoury JD, Tannir NM, Williams MD, et al. Landscape of DNA virus associations across human malignant cancers: Analysis of 3,775 cases using RNA-Seq. J Virol 2013;87:8916-26
11. Tang KW, Alaei-Mahabadi B, Samuelsson T, et al. The landscape of viral expression and host gene fusion and adaptation in human cancer. Nat Commun 2013;4:2513
12. Cosset E, Petty TJ, Dutoit V, et al. Comprehensive metagenomic analysis of glioblastoma reveals absence of known virus despite antiviral-like type I interferon gene response. Int J Cancer, in press
13. https://cghub.ucsc.edu
14. http://www.hudsonalpha.org/gsl/information/software/bam2fastq
15. Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011;27:863-4
16. Langmead B, Trapnell C, Pop M, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009;10:R25
17. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol Biol Evol 2013;30:772-80
18. Bexfield N, Kellam P. Metagenomics and the molecular identification of novel viruses. Vet J 2011;190:191-8
19. Boeckh M, Boivin G. Quantitation of cytomegalovirus: Methodologic aspects and clinical applications. Clin Microbiol Rev 1998;11: 533-54.