SeqMap 3

Introduction

It is important to determine where integrations take place when foreign DNA is introduced into target genomes. Profiling viral integration sites is much more critical in evaluating the safety of gene therapy viral vector. In recent years, LAM-PCR and nrLAM-PCR coupled with next-generation sequencing has become a standard approach to characterize viral integration sites in gene therapy. A few bioinformatics tools are available to analyze the sequencing data derived from high-throughput multiplexed sequencing of LAM-PCR/nrLAM-PCR amplicons. Here we implement a new bioinformatics pipeline, SeqMap3. Unlike the several published tools that use BLAST or BLAT to identify VIS, we instead utilize the well developed and widely used short reads alignment tools bowtie in SeqMap 3. It is orders of magnitude faster than BLAST and BLAT.

The above figure illustrates the strategies for identification of viral integration sites. SeqMap 3 is mainly designed for paired-end sequence data derived from amplicons of LAM-PCR or nrLAM-PCR with a structure as displayed in the top box. SepMap3 has been tested on data from nrLAM-PCR and LAM-PCR performed in 3' direction, but not yet on data from nrLAM-PCR and LAM-PCR performed in 5' direction.

Access to SeqMap 3


To login to SeqMap 3 you must use your NGVB account. To login you must use the email address and password you signed up with. This is so SeqMap can email you once your jobs are complete.