BS-virus-finder: virus integration calling using bisulfite sequencing data

Shengjie Gao; Xuesong Hu; Fengping Xu; Changduo Gao; Kai Xiong; Xiao Zhao; Haixiao Chen; Shancen Zhao; Mengyao Wang; Dongke Fu; Xiaohui Zhao; Jie Bai; Likai Mao; Bo Li; Song Wu; Jian Wang; Shengbin Li; Huangming Yang; Lars Bolund; Christian N S Pedersen

doi:10.1093/gigascience/gix123

BS-virus-finder: virus integration calling using bisulfite sequencing data

Shengjie Gao, Xuesong Hu, Fengping Xu, Changduo Gao, Kai Xiong, Xiao Zhao, Haixiao Chen, Shancen Zhao, Mengyao Wang, Dongke Fu, Xiaohui Zhao, Jie Bai, Likai Mao, Bo Li, Song Wu, Jian Wang, Shengbin Li, Huangming Yang, Lars Bolund, Christian N S Pedersen

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

2 Citations (Scopus)

Abstract

Background: DNA methylation plays a key role in the regulation of gene expression and carcinogenesis. Bisulfite sequencing studies mainly focus on calling single nucleotide polymorphism, different methylation region, and find allele-specific DNA methylation. Until now, only a few software tools have focused on virus integration using bisulfite sequencing data. Findings: We have developed a new and easy-to-use software tool, named BS-virus-finder (BSVF, RRID:SCR 015727), to detect viral integration breakpoints in whole human genomes. The tool is hosted at https://github.com/BGI-SZ/BSVF. Conclusions: BS-virus-finder demonstrates high sensitivity and specificity. It is useful in epigenetic studies and to reveal the relationship between viral integration and DNA methylation. BS-virus-finder is the first software tool to detect virus integration loci by using bisulfite sequencing data.

Original language	English
Journal	GigaScience
Volume	7
Issue	1
Pages (from-to)	1-7
Number of pages	7
ISSN	2047-217X
DOIs	https://doi.org/10.1093/gigascience/gix123
Publication status	Published - 1 Jan 2018

Keywords

Bisulfite sequencing
Carcinogenesis
Virus integration

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@article{5a8364dfc83449a8b7860cad6baaaa62,

title = "BS-virus-finder: virus integration calling using bisulfite sequencing data",

abstract = "Background: DNA methylation plays a key role in the regulation of gene expression and carcinogenesis. Bisulfite sequencing studies mainly focus on calling single nucleotide polymorphism, different methylation region, and find allele-specific DNA methylation. Until now, only a few software tools have focused on virus integration using bisulfite sequencing data. Findings: We have developed a new and easy-to-use software tool, named BS-virus-finder (BSVF, RRID:SCR 015727), to detect viral integration breakpoints in whole human genomes. The tool is hosted at https://github.com/BGI-SZ/BSVF. Conclusions: BS-virus-finder demonstrates high sensitivity and specificity. It is useful in epigenetic studies and to reveal the relationship between viral integration and DNA methylation. BS-virus-finder is the first software tool to detect virus integration loci by using bisulfite sequencing data.",

keywords = "Bisulfite sequencing, Carcinogenesis, Virus integration",

author = "Shengjie Gao and Xuesong Hu and Fengping Xu and Changduo Gao and Kai Xiong and Xiao Zhao and Haixiao Chen and Shancen Zhao and Mengyao Wang and Dongke Fu and Xiaohui Zhao and Jie Bai and Likai Mao and Bo Li and Song Wu and Jian Wang and Shengbin Li and Huangming Yang and Lars Bolund and Pedersen, \{Christian N S\}",

year = "2018",

month = jan,

day = "1",

doi = "10.1093/gigascience/gix123",

language = "English",

volume = "7",

pages = "1--7",

journal = "GigaScience",

issn = "2047-217X",

publisher = "Oxford University Press",

number = "1",

}

TY - JOUR

T1 - BS-virus-finder

T2 - virus integration calling using bisulfite sequencing data

AU - Gao, Shengjie

AU - Hu, Xuesong

AU - Xu, Fengping

AU - Gao, Changduo

AU - Xiong, Kai

AU - Zhao, Xiao

AU - Chen, Haixiao

AU - Zhao, Shancen

AU - Wang, Mengyao

AU - Fu, Dongke

AU - Zhao, Xiaohui

AU - Bai, Jie

AU - Mao, Likai

AU - Li, Bo

AU - Wu, Song

AU - Wang, Jian

AU - Li, Shengbin

AU - Yang, Huangming

AU - Bolund, Lars

AU - Pedersen, Christian N S

PY - 2018/1/1

Y1 - 2018/1/1

N2 - Background: DNA methylation plays a key role in the regulation of gene expression and carcinogenesis. Bisulfite sequencing studies mainly focus on calling single nucleotide polymorphism, different methylation region, and find allele-specific DNA methylation. Until now, only a few software tools have focused on virus integration using bisulfite sequencing data. Findings: We have developed a new and easy-to-use software tool, named BS-virus-finder (BSVF, RRID:SCR 015727), to detect viral integration breakpoints in whole human genomes. The tool is hosted at https://github.com/BGI-SZ/BSVF. Conclusions: BS-virus-finder demonstrates high sensitivity and specificity. It is useful in epigenetic studies and to reveal the relationship between viral integration and DNA methylation. BS-virus-finder is the first software tool to detect virus integration loci by using bisulfite sequencing data.

AB - Background: DNA methylation plays a key role in the regulation of gene expression and carcinogenesis. Bisulfite sequencing studies mainly focus on calling single nucleotide polymorphism, different methylation region, and find allele-specific DNA methylation. Until now, only a few software tools have focused on virus integration using bisulfite sequencing data. Findings: We have developed a new and easy-to-use software tool, named BS-virus-finder (BSVF, RRID:SCR 015727), to detect viral integration breakpoints in whole human genomes. The tool is hosted at https://github.com/BGI-SZ/BSVF. Conclusions: BS-virus-finder demonstrates high sensitivity and specificity. It is useful in epigenetic studies and to reveal the relationship between viral integration and DNA methylation. BS-virus-finder is the first software tool to detect virus integration loci by using bisulfite sequencing data.

KW - Bisulfite sequencing

KW - Carcinogenesis

KW - Virus integration

UR - https://www.scopus.com/pages/publications/85044588608

U2 - 10.1093/gigascience/gix123

DO - 10.1093/gigascience/gix123

M3 - Journal article

C2 - 29267855

SN - 2047-217X

VL - 7

SP - 1

EP - 7

JO - GigaScience

JF - GigaScience

IS - 1

ER -

BS-virus-finder: virus integration calling using bisulfite sequencing data

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