Prototyping GenoTHREAT a biosecurity solution for synthetic genomics

Virginia Polytechnic Institute And State University, Blacksburg VA

Investigators

Abstract

The Virginia Bioinformatics Institute at Virginia Tech is awarded a grant to develop GenoTHREAT, a software application to screen DNA sequences ordered from gene synthesis companies for the possible presence of potentially harmful sequences. GenoTHREAT implements the screening algorithm recommended by the Department of Health and Human Services in a document entitled "Screening Frameworks Guidance for Synthetic Double-Stranded DNA Providers." It is important to characterize the relationship between the computational cost of the sequence screening algorithm, the rate of false positives or innocuous sequences that are incorrectly red flagged, and the rate of false negatives or sequences of concern not detected by the screening algorithm. The screen is applied to a database composed of a mixture of publicly available sets of synthetic DNA sequences and annotated test cases designed for this project. This large scale analysis will lead to the determination of optimal screen parameters that represent an acceptable compromise between the security concerns of the government and the operational constraints of gene synthesis companies. The rapid progress in synthetic biology demonstrated by the recent publication of the first synthetic cell by Craig Venter and his team has raised biosecurity concerns among the public, its elected officials, and various administrations. This grant facilitates the adoption of DNA screening algorithm recommended by the federal government to detect, in the order books of gene synthesis companies, the presence of sequences of concern requiring further investigations. GenoTHREAT, the software developed with the grant, will be made broadly available (www.genothreat.org) to allow gene synthesis companies, users of synthetic DNA, or managers of bioinformatics resources for synthetic biology to implement the biosecurity screen recommended by the government. In order to provide another layer of biosecurity protection, GenoTHREAT will also be capable of screening DNA sequencing data. A sustainability plan that does not involve federal funding for the maintenance and future development of GenoTHREAT is being developed with industrial partners.