title: BATVI: Fast, sensitive and accurate detection of virus integrations.
abstract: BACKGROUND
  The study of virus integrations in human genome is important since virus integrations were shown to be associated with diseases. In the literature, few methods have been proposed that predict virus integrations using next generation sequencing datasets. Although they work, they are slow and are not very sensitive.
  
  
  CONCLUSIONS
  This paper introduces a new method BatVI to predict viral integrations. Our method uses a fast screening method to filter out chimeric reads containing possible viral integrations. Next, sensitive alignments of these candidate chimeric reads are called by BLAST. Chimeric reads that are co-localized in the human genome are clustered. Finally, by assembling the chimeric reads in each cluster, high confident virus integration sites are extracted.
  
  
  CONCLUSIONS
  We compared the performance of BatVI with existing methods VirusFinder and VirusSeq using both simulated and real-life datasets of liver cancer patients. BatVI ran an order of magnitude faster and was able to predict almost twice the number of true positives compared to other methods while maintaining a false positive rate less than 1%. For the liver cancer datasets, BatVI uncovered novel integrations to two important genes TERT and MLL4, which were missed by previous studies. Through gene expression data, we verified the correctness of these additional integrations. BatVI can be downloaded from http://biogpu.ddns.comp.nus.edu.sg/~ksung/batvi/index.html .
authors.affiliation: Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672, Singapore.|UAE University, PO Box, 17551, Al Ain, United Arab Emirates.
authors.forename: Chandana
authors.initials: C
authors.lastname: Tennakoon
authors.affiliation: Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672, Singapore. ksung@comp.nus.edu.sg.|Department of Computer Science, National Unversity of Singapore, Singapore, 117417, Singapore. ksung@comp.nus.edu.sg.
authors.forename: Wing Kin
authors.initials: WK
authors.lastname: Sung
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D004279:DNA, Viral / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D011495:Histone-Lysine N-Methyltransferase; D054884:Host-Pathogen Interactions / Q000235:genetics*; D006801:Humans; D008113:Liver Neoplasms / Q000175:diagnosis / Q000821:virology; D008962:Models, Theoretical; D017422:Sequence Analysis, DNA; D012984:Software; D019098:Telomerase / Q000235:genetics / Q000378:metabolism; D016662:Virus Integration
chemical_list: D004279:DNA, Viral; D004268:DNA-Binding Proteins; D011495:Histone-Lysine N-Methyltransferase; C530816:MLL4 protein, human; C509186:TERT protein, human; D019098:Telomerase
keywords: Alignment; NGS; Viral integration