SummonChimera infers integrated viral genomes with nucleotide precision from NGS data

BMC Bioinformatics

James M Pipas¹  Joshua P Katz¹ 

[1]Department of Biological Sciences, University of Pittsburgh, Pittsburgh 15260, PA, USA

关键词: Cancer;    Virus;    Integration;   

Others  :  1085433
DOI  :  10.1186/s12859-014-0348-4

 received in 2014-05-23, accepted in 2014-10-09,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Katz and Pipas; licensee BioMed Central Ltd.

【 图 表 】

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