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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
2012 Computer applications in the biosciences : CABIOS  
We developed a new algorithmic method, VirusSeq, for detecting known viruses and their integration sites in the human genome using next-generation sequencing data.  ...  VirusSeq can also perform this function using whole-genome sequencing data of human tissue.  ...  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  ... 
doi:10.1093/bioinformatics/bts665 pmid:23162058 pmcid:PMC3546792 fatcat:v2m53c73fra5hlz36ubgve4hea

VirusFinder: Software for Efficient and Accurate Detection of Viruses and Their Integration Sites in Host Genomes through Next Generation Sequencing Data

Qingguo Wang, Peilin Jia, Zhongming Zhao, Dongxiao Zhu
2013 PLoS ONE  
Here, we present a new tool, VirusFinder, for the identification of viruses and their integration sites in host genomes using NGS data, including whole transcriptome sequencing (RNA-Seq), whole genome  ...  Next generation sequencing (NGS) technologies allow us to explore virus interactions with host genomes that lead to carcinogenesis or other diseases; however, this effort is largely hindered by the dearth  ...  Acknowledgments We are grateful to Dr. Eric J. Duncavage for sharing with us their data. We also thank Drs. Huy Vuong, Jingchun Sun, and the authors of PathSeq and RINS for their great assistance.  ... 
doi:10.1371/journal.pone.0064465 pmid:23717618 pmcid:PMC3663743 fatcat:bxpilc5otfc7pbyo7movvdycxa

VERSE: a novel approach to detect virus integration in host genomes through reference genome customization

Qingguo Wang, Peilin Jia, Zhongming Zhao
2015 Genome Medicine  
Fueled by widespread applications of high-throughput next generation sequencing (NGS) technologies and urgent need to counter threats of pathogenic viruses, large-scale studies were conducted recently  ...  Using 19 human tumors and cancer cell lines as test data, we demonstrated that VERSE substantially enhanced the sensitivity of virus integration site detection.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.1186/s13073-015-0126-6 pmid:25699093 pmcid:PMC4333248 fatcat:2sdjhk6xn5eizak4fkj6lu6e5e

Detection of human papillomavirus in cases of head and neck squamous cell carcinoma by RNA-seq and VirTect

Atlas Khan, Qian Liu, Xuelian Chen, Andres Stucky, Parish P. Sedghizadeh, Daniel Adelpour, Xi Zhang, Kai Wang, Jiang F. Zhong
2019 Molecular Oncology  
Next-generation sequencing provides an opportunity to detect viral species from RNA-seq data of human tissues, but existing computational approaches do not perform optimally on clinical samples.  ...  We developed a bioinformatic method called VirTect for detecting viruses in neoplastic human tissues using RNA-seq data.  ...  Acknowledgements The results published here are in part based upon data generated by TCGA, managed by the NCI and NHGRI. We are grateful to TCGA for this source of data.  ... 
doi:10.1002/1878-0261.12435 pmid:30597724 pmcid:PMC6441885 fatcat:wxtxixwnrjcblan4m4mfju6ryq

VirTect: a computational method for detecting virus species from RNA-Seq and its application in head and neck squamous cell carcinoma [article]

Atlas Khan, Qian Liu, Xuelian Chen, Yunjing Zeng, Andres Stucky, Parish P. Sedghizadeh, Daniel Adelpour, Xi Zhang, Kai Wang, Jiang F. Zhong
2018 bioRxiv   pre-print
Next generation sequencing (NGS) provides an opportunity to detect viral species from RNA-seq data on human tissues, but existing computational approaches do not perform optimally on clinical samples.  ...  We developed a bioinformatics method called VirTect for detecting viruses in neoplastic human tissues using RNA-seq data.  ...  The main limitation of VirTect is that it depends on a database of all known viruses, which is used to nominate candidate viruses in human cancer tissue.  ... 
doi:10.1101/272278 fatcat:fh54wfjwc5apxlsxa5tcxhnuwa

HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data

Saurabh Baheti, Xiaojia Tang, Daniel R. O'Brien, Nicholas Chia, Lewis R. Roberts, Heidi Nelson, Judy C. Boughey, Liewei Wang, Matthew P. Goetz, Jean-Pierre A. Kocher, Krishna R. Kalari
2018 BMC Bioinformatics  
The integration of viruses into the human genome is associated with multiple cancers, and these can now be detected using next-generation sequencing methods such as whole genome sequencing and RNA-sequencing  ...  Results: We designed a novel computational workflow, HGT-ID, to identify the integration of viruses into the human genome using the sequencing data.  ...  Conclusion HGT-ID is a novel computational workflow to detect the integration of viruses in the human genome using the sequencing data.  ... 
doi:10.1186/s12859-018-2260-9 pmid:30016933 pmcid:PMC6050683 fatcat:o6aty7lqdjfvdnejfzdy7fx3te

Lack of Viral Load Within Chronic Lymphoproliferative Disorder of Natural Killer Cells: What Is Outside the Leukemic Clone?

Edoardo Giussani, Andrea Binatti, Giulia Calabretto, Vanessa Rebecca Gasparini, Antonella Teramo, Cristina Vicenzetto, Gregorio Barilà, Monica Facco, Alessandro Coppe, Gianpietro Semenzato, Stefania Bortoluzzi, Renato Zambello
2021 Frontiers in Oncology  
We next present original results of whole exome sequencing data analysis that failed to identify viral sequences in CLPD-NK.  ...  In this perspective, we revise the lines of evidence that suggested a pathogenetic role in LGLL of the exposure to retroviruses and that identified Epstein Barr Virus (EBV) in other NK cell leukemias and  ...  , particularly viruses, in cancer clones and also to define possible sites of integration in the host genome or their presence in episomal forms (10, 11) .  ... 
doi:10.3389/fonc.2020.613570 pmid:33585237 pmcid:PMC7873950 fatcat:pl36le7pt5fmze4vtl4urg5tza

Finding the lost treasures in exome sequencing data

David C. Samuels, Leng Han, Jiang Li, Sheng Quanghu, Travis A. Clark, Yu Shyr, Yan Guo
2013 Trends in Genetics  
All of these can be used for reliable data mining, extending the utility of exome sequencing.  ...  Largescale exome sequencing data repositories, such as The Cancer Genome Atlas (TCGA), the 1000 Genomes Project, National Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project, and The Sequence  ...  For example, PathSeq was developed to identify viruses through sequencing data of human samples [7] . VirusSeq was developed to identify viral sequences using exome-sequencing or RNAseq data [8] .  ... 
doi:10.1016/j.tig.2013.07.006 pmid:23972387 pmcid:PMC3926691 fatcat:57z5dooounavzpjdqsbvia4lgu

Viral expression associated with gastrointestinal adenocarcinomas in TCGA high-throughput sequencing data

Daria Salyakina, Nicholas F Tsinoremas
2013 Human Genomics  
Conclusions: Our comprehensive screening for viruses in multiple cancer types using next-generation sequencing data clearly demonstrates the presence of viral sequences in GIA.  ...  Up to 20% of cancers worldwide are thought to be associated with microbial pathogens, including bacteria and viruses.  ...  This work was supported by the Center for Computational Salyakina and Tsinoremas Human Genomics 2013, 7:23 Page 10 of 12 http://www.humgenomics.com/content/7/1/23  ... 
doi:10.1186/1479-7364-7-23 pmid:24279398 pmcid:PMC3906926 fatcat:hg6a3vmogfdsdaie7c2f3kcsii

SurVirus: a repeat-aware virus integration caller

Ramesh Rajaby, Yi Zhou, Yifan Meng, Xi Zeng, Guoliang Li, Peng Wu, Wing-Kin Sung
2021 Nucleic Acids Research  
A significant portion of human cancers are due to viruses integrating into human genomes.  ...  Virus integrations can be called by analysing second generation high-throughput sequencing datasets.  ...  ACKNOWLEDGEMENTS We would to acknowledge to thank Chen Xun for its help in the usage of VIcaller.  ... 
doi:10.1093/nar/gkaa1237 pmid:33444454 fatcat:djwk5bbexjckzkuwf2wqp2yf3a

STEAK: A specific tool for transposable elements and retrovirus detection in high-throughput sequencing data

Cindy G. Santander, Philippe Gambron, Emanuele Marchi, Timokratis Karamitros, Aris Katzourakis, Gkikas Magiorkinis
2017 Virus Evolution  
The advancements of high-throughput genomics have unveiled much about the human genome highlighting the importance of variations between individuals and their contribution to disease.  ...  Here we describe our program STEAK, a massively parallel software designed to detect chimeric reads in high-throughput sequencing data for a broad number of applications such as identifying presence/absence  ...  Acknowledgements We thank our colleagues in the Applied Evolutionary Virology and Paleovirology groups who have supported us and provided us feedback during the development of STEAK.  ... 
doi:10.1093/ve/vex023 pmid:28948042 pmcid:PMC5597868 fatcat:4fybx75zsfhdvckze67nxs7h2u

Alternative applications for distinct RNA sequencing strategies

Leng Han, Kasey C. Vickers, David C. Samuels, Yan Guo
2014 Briefings in Bioinformatics  
We detail how RNAseq can be used to identify allele-specific expression, single-nucleotide polymorphisms and somatic mutations and discuss the benefits and limitations of using RNAseq to monitor DNA characteristics  ...  Here we review the current state of the art in transcriptome sequencing and address epigenetic regulation, quantification of transcription activation, RNAseq output and a diverse set of applications for  ...  Acknowledgments The authors would like to thank Leslie A. Roteta and Margot Bjoring for their assistance in drafting the review.  ... 
doi:10.1093/bib/bbu032 pmid:25246237 pmcid:PMC4542857 fatcat:rtr2qqlwsjawphxt2k3cmdyf3q

Genomic characterization of human papillomavirus-positive and -negative human squamous cell cancer cell lines

Nene N. Kalu, Tuhina Mazumdar, Shaohua Peng, Li Shen, Vaishnavi Sambandam, Xiayu Rao, Yuanxin Xi, Lerong Li, Yuan Qi, Frederico O. Gleber-Netto, Ameeta Patel, Jing Wang (+4 others)
2017 OncoTarget  
Human cancer cell lines are the most frequently used preclinical models in the study of cancer biology and the development of therapeutics.  ...  We used over 700 human tumors for comparison. Mutation patterns in the cell lines were similar to those of human tumors.  ...  Finally, HPV integration sites were identified using VirusSeq and reported if there were at least 4 supporting discordant read pairs.  ... 
doi:10.18632/oncotarget.21174 pmid:29156801 pmcid:PMC5689691 fatcat:jps6dckuwvexfo6eckdhcwmzaa

Human papillomavirus type 16 sub-lineages and integration in cancer [article]

Robert Jackson, Alejandro Ortigas-Vásquez, Ingeborg Zehbe
2020 bioRxiv   pre-print
Next-generation sequencing (NGS) data confirmed a transcriptomic profile of increased proliferation and chromosomal instability−both hallmarks of cancer.  ...  Multiple DNA viruses such as Epstein-Barr virus, hepatitis B virus, and human papillomavirus (HPV) can invade their host genome, as "genomic parasites".  ...  Acknowledgements 468 The results reported here are based upon data generated by The Cancer Genome Atlas 469 Research Network (cancergenome.nih.gov) and we are grateful to the participants and Network  ... 
doi:10.1101/2020.06.25.162958 fatcat:clwczn6a5fejddmyvncv242pcy

ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer

Nam-phuong D Nguyen, Viraj Deshpande, Jens Luebeck, Paul S Mischel, Vineet Bafna
2018 Nucleic Acids Research  
The integration of viral sequences into the host genome is an important driver of tumorigenesis in many viral mediated cancers, notably cervical cancer and hepatocellular carcinoma.  ...  to the pathogenesis of HPVassociated cervical cancers.  ...  The terms of this arrangement have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies.  ... 
doi:10.1093/nar/gky180 pmid:29579309 fatcat:qv6h7bbrybafdfzmtyaodyt5uq
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