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GeIST: a command-line pipeline for DNA integration mapping

Wednesday, September 24, 2014 — Poster Session IV

10:00 a.m. –12:00 p.m.

FAES Academic Center



* FARE Award Winner


  • M.C. LaFave
  • G.K. Varshney
  • T.G. Wolfsberg
  • A.D. Baxevanis
  • S.M. Burgess


The integration of foreign DNA into target genomes is useful in many experimental settings; gene therapy, gene/enhancer traps, and retroviral mutagenesis all take advantage of this approach. In such studies, it is important to determine where the integrations take place. We previously developed a high-throughput method capable of identifying millions of integration sites, and now present the software designed to analyze the results of this method. The Genomic Integration Site Tracker (GeIST) is an automated command-line pipeline designed to interpret ligation-mediated PCR samples from Illumina MiSeq and HiSeq technologies. It identifies DNA integration sites and uses sequence barcodes to group them by sample. GeIST includes support for Tol2- and Ac/Ds-based vectors, as well as murine leukemia virus and adeno-associated virus. We optimized integration recovery for each of these four vectors by analyzing experimental data. GeIST is available at

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