ArticleBMC bioinformatics2014
SummonChimera infers integrated viral genomes with nucleotide precision from NGS data.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Recurrent integration of human papillomavirus genomes at transcriptional regulatory hubs.NPJ genomic medicine · 2021Article
- SurVirus: a repeat-aware virus integration caller.Nucleic acids research · 2021Article
- ViR: a tool to solve intrasample variability in the prediction of viral integration sites using whole genome sequencing data.BMC bioinformatics · 2021Article
- Intra-host changes in Kaposi sarcoma-associated herpesvirus genomes in Ugandan adults with Kaposi sarcoma.PLoS pathogens · 2021Article
- A virome-wide clonal integration analysis platform for discovering cancer viral etiology.Genome research · 2019Article
- Genome-wide profiling of human papillomavirus DNA integration in liquid-based cytology specimens from a Gabonese female population using HPV capture technology.Scientific reports · 2019Article
- Viral sequences in human cancer.Virology · 2018Article
- Article
- Functional variants of human papillomavirus type 16 demonstrate host genome integration and transcriptional alterations corresponding to their unique cancer epidemiology.BMC genomics · 2016Article
- HeLa nucleic acid contamination in the cancer genome atlas leads to the misidentification of human papillomavirus 18.Journal of virology · 2015Article
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Authors and funding
2 authors.
Funding
Abstract
backgroundViral 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.
resultsSummonchimera 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.
conclusionsSummonChimera 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.
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