Identifying viral integration sites using SeqMap 2.0

Troy B. Hawkins, Jessica Dantzer, Brandon Peters, Mary Dinauer, Keithanne Mockaitis, Sean Mooney, Kenneth Cornetta

Research output: Contribution to journalArticlepeer-review

27 Scopus citations

Abstract

Summary: Retroviral integration has been implicated in several biomedical applications, including identification of cancerassociated genes and malignant transformation in gene therapy clinical trials. We introduce an efficient and scalable method for fast identification of viral vector integration sites from long read high-throughput sequencing. Individual sequence reads are masked to remove non-genomic sequence, aligned to the host genome and assembled into contiguous fragments used to pinpoint the position of integration.

Original languageEnglish (US)
Article numberbtq722
Pages (from-to)720-722
Number of pages3
JournalBioinformatics
Volume27
Issue number5
DOIs
StatePublished - Mar 2011

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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