title: SummonChimera infers integrated viral genomes with nucleotide precision from NGS data.
abstract: BACKGROUND
  Viral integration into a host genome is defined by two chimeric junctions that join viral and host DNA. Recently, computational tools have been developed that utilize NGS data to detect chimeric junctions. These methods identify individual viral-host junctions but do not associate chimeric pairs as an integration event. Without knowing the chimeric boundaries of an integration, its genetic content cannot be determined.
  
  
  RESULTS
  Summonchimera is a Perl program that associates chimera pairs to infer the complete viral genomic integration event to the nucleotide level within single or paired-end NGS data. SummonChimera integration prediction was verified on a set of single-end IonTorrent reads from a purified Salmonella bacterium with an integrated bacteriophage. Furthermore, SummonChimera predicted integrations from experimentally verified Hepatitis B Virus chimeras within a paired-end Whole Genome Sequencing hepatocellular carcinoma tumor database.
  
  
  CONCLUSIONS
  SummonChimera identified all experimentally verified chimeras detected by current computational methods. Further, SummonChimera integration inference precisely predicted bacteriophage integration. The application of SummonChimera to cancer NGS accurately identifies deletion of host and viral sequence during integration. The precise nucleotide determination of an integration allows prediction of viral and cellular gene transcription patterns.
authors.affiliation: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA. joshpk105@gmail.com.
authors.forename: Joshua P
authors.initials: JP
authors.lastname: Katz
authors.affiliation: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA. pipas@pitt.edu.
authors.forename: James M
authors.initials: JM
authors.lastname: Pipas
mesh_terms: D001435:Bacteriophages / Q000235:genetics; D006528:Carcinoma, Hepatocellular / Q000821:virology; D016679:Genome, Viral; D023281:Genomics; D006515:Hepatitis B virus; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008113:Liver Neoplasms / Q000821:virology; D009711:Nucleotides / Q000032:analysis; D012475:Salmonella / Q000821:virology; D012984:Software; D016662:Virus Integration
chemical_list: D009711:Nucleotides