Identifying viral integration sites using SeqMap 2.0.
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.


METHODS
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/.
Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA. troyhawk@iupui.edu
Troy B
TB
Hawkins
Jessica
J
Dantzer
Brandon
B
Peters
Mary
M
Dinauer
Keithanne
K
Mockaitis
Sean
S
Mooney
Kenneth
K
Cornetta
D016000:Cluster Analysis; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D020407:Internet; D012190:Retroviridae / Q000235:genetics* / Q000502:physiology; D016415:Sequence Alignment; D012984:Software; D016662:Virus Integration
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