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INSIDER: alignment-free detection of foreign DNA sequences
Aidan P Tay1,2, Brendan Hosking1, Cameron Hosking1
1Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, New South Wales, Sydney, Australia.
Computational and Structural Biotechnology Journal
|July 21, 2021
Summary
We developed INSIDER, a tool to detect foreign DNA in genomes. It identifies inserted sequences by analyzing k-mer signatures, aiding in biosecurity and health applications like antimicrobial resistance detection.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Identifying foreign DNA in genomes is crucial for health and biosecurity.
- Current methods struggle with poorly characterized genomes or unknown inserted sequences.
- Applications include antimicrobial resistance (AMR) detection and gene drive monitoring.
Purpose of the Study:
- To develop a robust method for detecting foreign DNA insertions in host genomes.
- To address limitations in identifying integrated sequences in poorly characterized organisms.
- To enhance biosecurity monitoring and health applications.
Main Methods:
- Developed the INserted Sequence Information DEtectoR (INSIDER) tool.
- INSIDER analyzes whole genome sequencing data.
- Identifies foreign DNA by detecting significant shifts in k-mer signatures.
Main Results:
- Successfully separated integrated DNA from normal genomic sequences using a synthetic dataset of yeast with a CRISPR-Cas gene drive.
- Demonstrated proof-of-concept by detecting an AMR plasmid in *Citrobacter freundii* patient isolate whole genome sequencing data.
- INSIDER effectively identifies foreign DNA segments based on k-mer signature shifts.
Conclusions:
- INSIDER streamlines the identification of integrated DNA in poorly characterized species.
- The tool enhances the monitoring of emerging biosecurity threats and aids in health applications.
- INSIDER provides a crucial capability for detecting foreign DNA of unknown origin.
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