IntegrationMap

IntegrationMap maps genomic integration sites produced by viral vectors and viruses to characterize their locations relative to genes, transcriptional units, and transcription start sites for analysis of retroviral vector-mediated gene transfer.

Key Features:

• Automated Genomic Mapping: Automates mapping of integration sites and reports whether integrations occur within or near genes, specifies gene names, and pinpoints exact localizations within transcriptional units.
• Comprehensive Data Retrieval: Retrieves parameters such as the distance from the transcription start site to the integration point to inform potential functional impacts of insertions.
• High Sensitivity and Speed: Processes sequences with high sensitivity and operates 15 times faster while maintaining equal specificity, leveraging IntegrationSeq to trim sequences to valid integration data for further processing.
• Standardization and Validation: Enables standardized comparison across large datasets and was validated on 259 files from integration site analysis (LM-PCR), producing output files 99.8% identical to those generated by slower conventional mapping tools like ENSEMBL.

Scientific Applications:

• Gene therapy safety assessment: Characterizes integration-site distributions for assessing safety and efficacy of viral vector–mediated gene transfer.
• Viral vector integration profiling: Profiles integration locations of viral vectors and viruses relative to genes and transcriptional units.
• Comparative high-throughput analysis: Enables systematic comparison of insertion site data across studies and benchmarking of mapping methods using LM-PCR datasets and ENSEMBL outputs.

Methodology:

IntegrationSeq trims sequences to yield valid integration sequences, and IntegrationMap automatically maps those sequences and retrieves detailed genomic information about the integrations.