[Paper Review] A system capable of verifiably and privately screening global DNA synthesis

Carsten Baum, Jens Berlips+29 more|arXiv (Cornell University)|Mar 20, 2024

DNA and Biological Computing7 citations

TL;DR

The paper presents SecureDNA, a privacy-preserving system that verifiably screens all DNA synthesis orders against a current database of controlled sequences, scalable to 67 million nucleotides across major regions.

ABSTRACT

Printing custom DNA sequences is essential to scientific and biomedical research, but the technology can be used to manufacture plagues as well as cures. Just as ink printers recognize and reject attempts to counterfeit money, DNA synthesizers and assemblers should deny unauthorized requests to make viral DNA that could be misused. There are three complications. First, we don't need to quickly update printers to deal with newly discovered currencies, whereas we regularly learn of new potential pandemic viruses and other biological threats. Second, convincing counterfeit bills can't be printed in small pieces and taped together, while preventing the distributed synthesis and subsequent re-assembly of controlled sequences will require tracking which DNA fragments have been ordered across all providers and benchtop devices while protecting legitimate customer privacy. Finally, counterfeiting can at worst undermine faith in currency, whereas unauthorized DNA synthesis could be used to deliberately cause pandemics. Here we describe SecureDNA, a free, privacy-preserving, and fully automated system capable of verifiably screening all DNA synthesis orders of 30+ nucleotides against an up-to-date database of controlled sequences, and its operational performance and specificity when applied to 67 million nucleotides of DNA synthesized by providers in the United States, Europe, and China.

Motivation & Objective

• Motivate safe DNA synthesis by preventing unauthorized production of harmful sequences while protecting legitimate customers’ privacy.
• Develop a free, automated system that can screen orders of 30+ nucleotides against an up-to-date controlled-sequences database.
• Ensure verifiability of screening decisions and scalability across global synthesis providers.

Proposed method

• Describe SecureDNA’s privacy-preserving screening workflow against an up-to-date database of controlled sequences.
• Provide automated, verifiable checks that deny unauthorized requests while preserving user privacy.
• Demonstrate performance and specificity on a dataset totaling 67 million nucleotides from providers in the US, Europe, and China.

Experimental results

Research questions

• RQ1 Can a privacy-preserving system verifiably screen DNA synthesis orders against a controlled-sequences database at global scale?
• RQ2 How does the system perform in terms of specificity and operational throughput on large, real-world synthesis data?
• RQ3 What privacy guarantees are achievable for legitimate customers within a global DNA synthesis screening pipeline?

Key findings

• SecureDNA is a free, privacy-preserving, and fully automated system for screening DNA synthesis orders.
• The system screens orders of 30+ nucleotides against an up-to-date database of controlled sequences.
• Operational testing covered 67 million nucleotides of DNA synthesized by providers in the United States, Europe, and China.
• The paper reports on operational performance and specificity of SecureDNA.