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 journalArticle

23 Citations (Scopus)

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

Fingerprint

Virus Integration
Genetic Therapy
Clinical Trials
Genome
Genes
Gene Therapy
Gene therapy
Biomedical Applications
Sequencing
High Throughput
Fragment
Throughput
Gene

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Hawkins, T. B., Dantzer, J., Peters, B., Dinauer, M., Mockaitis, K., Mooney, S., & Cornetta, K. (2011). Identifying viral integration sites using SeqMap 2.0. Bioinformatics, 27(5), 720-722. [btq722]. https://doi.org/10.1093/bioinformatics/btq722

Identifying viral integration sites using SeqMap 2.0. / Hawkins, Troy B.; Dantzer, Jessica; Peters, Brandon; Dinauer, Mary; Mockaitis, Keithanne; Mooney, Sean; Cornetta, Kenneth.

In: Bioinformatics, Vol. 27, No. 5, btq722, 03.2011, p. 720-722.

Research output: Contribution to journalArticle

Hawkins, TB, Dantzer, J, Peters, B, Dinauer, M, Mockaitis, K, Mooney, S & Cornetta, K 2011, 'Identifying viral integration sites using SeqMap 2.0', Bioinformatics, vol. 27, no. 5, btq722, pp. 720-722. https://doi.org/10.1093/bioinformatics/btq722
Hawkins TB, Dantzer J, Peters B, Dinauer M, Mockaitis K, Mooney S et al. Identifying viral integration sites using SeqMap 2.0. Bioinformatics. 2011 Mar;27(5):720-722. btq722. https://doi.org/10.1093/bioinformatics/btq722
Hawkins, Troy B. ; Dantzer, Jessica ; Peters, Brandon ; Dinauer, Mary ; Mockaitis, Keithanne ; Mooney, Sean ; Cornetta, Kenneth. / Identifying viral integration sites using SeqMap 2.0. In: Bioinformatics. 2011 ; Vol. 27, No. 5. pp. 720-722.
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