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Synsor: a tool for alignment-free detection of engineered DNA sequences.

Aidan P Tay^1,2, Kieran Didi¹, Anuradha Wickramarachchi¹

¹Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney, NSW, Australia.

Frontiers in Bioengineering and Biotechnology

|July 29, 2024

Summary

Scientists developed Synsor, a new tool to detect engineered DNA in environmental and biological samples. This artificial neural network accurately identifies synthetic DNA, aiding in monitoring biological threats and public trust in genetic technologies.

Keywords:

alignment-free biosecurity biothreat detection deep learning engineered DNA

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Area of Science:

Synthetic biology
Bioinformatics
Genomics

Background:

Engineered DNA offers benefits like bioproduction but poses risks from misuse or environmental release.
Monitoring engineered DNA is vital for detecting biological threats and public acceptance of genetic technologies.

Purpose of the Study:

To develop a tool for identifying engineered DNA sequences in high-throughput sequencing data.
To enable routine and timely detection of emerging biological threats.

Main Methods:

Developed Synsor, a tool leveraging k-mer signature differences and an artificial neural network.
Trained and validated the model using natural plasmid and engineered vector sequences.
Applied Synsor to analyze genomic and metagenomic data from yeast and wastewater samples.

Main Results:

Synsor achieves >99% accuracy in identifying engineered DNA.
Demonstrated Synsor's capability to detect genetically engineered organisms.
Showcased Synsor's ability to pinpoint engineered DNA introduction sites in environmental samples.

Conclusions:

Synsor is a powerful tool for identifying engineered DNA in complex biological and environmental systems.
Facilitates enhanced monitoring of emerging biological threats.
Aids in improving public trust and acceptance of genetic technologies.