VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue

doi:10.1093/bioinformatics/bts665

. 2013 Jan 15;29(2):266-7.

doi: 10.1093/bioinformatics/bts665. Epub 2012 Nov 17.

VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue

Yunxin Chen¹, Hui Yao, Erika J Thompson, Nizar M Tannir, John N Weinstein, Xiaoping Su

Affiliations

PMID: 23162058
PMCID: PMC3546792
DOI: 10.1093/bioinformatics/bts665

VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue

Yunxin Chen et al. Bioinformatics. 2013.

. 2013 Jan 15;29(2):266-7.

doi: 10.1093/bioinformatics/bts665. Epub 2012 Nov 17.

Authors

Yunxin Chen¹, Hui Yao, Erika J Thompson, Nizar M Tannir, John N Weinstein, Xiaoping Su

Affiliation

¹ Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

PMID: 23162058
PMCID: PMC3546792
DOI: 10.1093/bioinformatics/bts665

Abstract

Summary: We developed a new algorithmic method, VirusSeq, for detecting known viruses and their integration sites in the human genome using next-generation sequencing data. We evaluated VirusSeq on whole-transcriptome sequencing (RNA-Seq) data of 256 human cancer samples from The Cancer Genome Atlas. Using these data, we showed that VirusSeq accurately detects the known viruses and their integration sites with high sensitivity and specificity. VirusSeq can also perform this function using whole-genome sequencing data of human tissue.

Availability: VirusSeq has been implemented in PERL and is available at http://odin.mdacc.tmc.edu/∼xsu1/VirusSeq.html.

Contact: xsu1@mdanderson.org

Supplementary information: Supplementary data are available at Bioinformatics online.

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References

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1. Ferber MJ, et al. Integrations of the hepatitis B virus (HBV) and human papillomavirus (HPV) into the human telomerase reverse transcriptase (hTERT) gene in liver and cervical cancers. Oncogene. 2003;22:3813–3820. - PubMed
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1. Isakov O, et al. Pathogen detection using short-RNA deep sequencing subtraction and assembly. Bioinformatics. 2011;27:2027–2030. - PMC - PubMed

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[1] Feng H, et al. Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science. 2008;319:1096–1100. - PMC - PubMed

[2] Feng H, et al. Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science. 2008;319:1096–1100. - PMC - PubMed

[3] Ferber MJ, et al. Integrations of the hepatitis B virus (HBV) and human papillomavirus (HPV) into the human telomerase reverse transcriptase (hTERT) gene in liver and cervical cancers. Oncogene. 2003;22:3813–3820. - PubMed

[4] Ferber MJ, et al. Integrations of the hepatitis B virus (HBV) and human papillomavirus (HPV) into the human telomerase reverse transcriptase (hTERT) gene in liver and cervical cancers. Oncogene. 2003;22:3813–3820. - PubMed

[5] Hausen Z. The search for infectious causes of human cancers: where and why. Virology. 2009;329:1–10. - PubMed

[6] Hausen Z. The search for infectious causes of human cancers: where and why. Virology. 2009;329:1–10. - PubMed

[7] Hiller LW, et al. Whole-genome sequencing and variant discovery in C. elegans. Nat. Methods. 2008;5:183–188. - PubMed

[8] Hiller LW, et al. Whole-genome sequencing and variant discovery in C. elegans. Nat. Methods. 2008;5:183–188. - PubMed

[9] Isakov O, et al. Pathogen detection using short-RNA deep sequencing subtraction and assembly. Bioinformatics. 2011;27:2027–2030. - PMC - PubMed

[10] Isakov O, et al. Pathogen detection using short-RNA deep sequencing subtraction and assembly. Bioinformatics. 2011;27:2027–2030. - PMC - PubMed

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VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue

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VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue

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