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

Yunxin Chen; Hui Yao; Erika J. Thompson; Nizar M. Tannir; John N. Weinstein; Xiaoping Su

doi:10.1093/bioinformatics/bts665

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

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

Research output: Contribution to journal › Article › peer-review

120 Scopus citations

Abstract

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.

Original language	English (US)
Pages (from-to)	266-267
Number of pages	2
Journal	Bioinformatics
Volume	29
Issue number	2
DOIs	https://doi.org/10.1093/bioinformatics/bts665
State	Published - Jan 15 2013

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/bts665

Cite this

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title = "VirusSeq: Software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue",

abstract = "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.",

author = "Yunxin Chen and Hui Yao and Thompson, {Erika J.} and Tannir, {Nizar M.} and Weinstein, {John N.} and Xiaoping Su",

note = "Funding Information: This work was supported in part by the National Cancer Institute, U.S. National Institutes of Health, through grant U24CA143883 for TCGA, and grant P30 CA016672, the Cancer Center Support Grant to The University of Texas MD Anderson Cancer Center; also by the National Center for Research Resources through grant UL1TR000371; and the H. A. and Mary K. Chapman Foundation and the Michael and Susan Dell Foundation.",

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AU - Tannir, Nizar M.

AU - Weinstein, John N.

AU - Su, Xiaoping

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

Abstract

ASJC Scopus subject areas

MD Anderson CCSG core facilities

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