GeIST

GeIST identifies and maps DNA integration sites genome-wide at base-pair resolution to analyze insertion events in multiplexed barcoded samples.

Key Features:

• Genome-wide base-pair resolution mapping: Identifies and maps DNA integration sites across the genome at single-base resolution in multiplexed barcoded samples.
• High-throughput scaling: Processes and maps millions of integration events from multiplexed samples.
• Multi-vector support: Detects integrations from murine leukemia virus, adeno-associated virus, Tol2 transposons, and Ac/Ds transposons and can be adapted for other inserted elements.
• Sequencing and cloning artifact handling: Implements steps to robustly handle sequencing and cloning artifacts common in high-throughput integration assays.
• Implementation: Uses Bash shell scripting and Perl for processing large integration assay datasets.
• Version: Version 2.1.0 provides enhanced adaptability for multiple delivery vectors.

Scientific Applications:

• Insertional mutagenesis screens: Maps integration sites to identify mutagenic insertion events across genomes.
• Gene and enhancer trap studies: Localizes insertions for gene- and enhancer-trap experiments to link integration sites to genomic features.
• Gene therapy vector analysis: Characterizes integration site distributions for gene therapy delivery vectors including adeno-associated virus and murine leukemia virus.

Methodology:

Computational implementation combines Bash shell scripting and Perl programming to process large integration assay datasets and address sequencing and cloning artifacts.