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Adler A, Bader JS, Basnight B, Booth BW, Cai J, Cho E, Collins JH, Ge Y, Grothendieck J, Keating K, Marshall T, Persikov A, Scott H, Siegelmann R, Singh M, Taggart A, Toll B, Wan KH, Wyschogrod D, Yaman F, Young EM, Celniker SE, Roehner N. Ensemble Detection of DNA Engineering Signatures. ACS Synth Biol 2024; 13:1105-1115. [PMID: 38468602 DOI: 10.1021/acssynbio.3c00398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Synthetic biology is creating genetically engineered organisms at an increasing rate for many potentially valuable applications, but this potential comes with the risk of misuse or accidental release. To begin to address this issue, we have developed a system called GUARDIAN that can automatically detect signatures of engineering in DNA sequencing data, and we have conducted a blinded test of this system using a curated Test and Evaluation (T&E) data set. GUARDIAN uses an ensemble approach based on the guiding principle that no single approach is likely to be able to detect engineering with perfect accuracy. Critically, ensembling enables GUARDIAN to detect sequence inserts in 13 target organisms with a high degree of specificity that requires no subject matter expert (SME) review.
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Affiliation(s)
- Aaron Adler
- Raytheon BBN, Cambridge, Massachusetts 02138, United States
| | - Joel S Bader
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Brian Basnight
- Raytheon BBN, Cambridge, Massachusetts 02138, United States
| | - Benjamin W Booth
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jitong Cai
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Elizabeth Cho
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joseph H Collins
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, United States
| | - Yuchen Ge
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | | | - Kevin Keating
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, United States
| | - Tyler Marshall
- Raytheon BBN, Cambridge, Massachusetts 02138, United States
| | - Anton Persikov
- Department of Computer Science, Princeton University, Princeton, New Jersey 08544, United States
| | - Helen Scott
- Raytheon BBN, Cambridge, Massachusetts 02138, United States
| | - Roy Siegelmann
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Mona Singh
- Department of Computer Science, Princeton University, Princeton, New Jersey 08544, United States
| | | | - Benjamin Toll
- Raytheon BBN, Cambridge, Massachusetts 02138, United States
| | - Kenneth H Wan
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | | | - Fusun Yaman
- Raytheon BBN, Cambridge, Massachusetts 02138, United States
| | - Eric M Young
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, United States
| | - Susan E Celniker
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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