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Updated: Jun 5, 2026

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
Published on: March 22, 2016
Identifying viral integration sites using SeqMap 2.0
Troy B Hawkins1, Jessica Dantzer, Brandon Peters
1Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA. troyhawk@iupui.edu
Unlabelled:
Retroviral integration has been implicated in several biomedical applications, including identification of cancer-associated 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.
Availability And Implementation:
The method is implemented in a publicly accessible web server platform, SeqMap 2.0, containing analysis tools and both private and shared lab workspaces that facilitate collaboration among researchers. Available at http://seqmap.compbio.iupui.edu/.
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