Prevalence of errors in lab-made plasmids across the globe

Bai, X.; Hong, J. F.; Yu, S.; Hu, D. Y.; Chen, A. Y.; Rich, C. A.; Shi, S. J.; Xu, S. Y.; Croucher, D. M.; Mussar, K. J.; Meng, D. W.; Chen, J. L.; Lahn, B. T.

doi:10.1101/2024.06.17.596931

bioRxiv · 10.1101/2024.06.17.596931

Prevalence of errors in lab-made plasmids across the globe

Bai, X.·Hong, J. F.·Yu, S.·Hu, D. Y.·Chen, A. Y.·Rich, C. A.·Shi, S. J.·Xu, S. Y.·Croucher, D. M.·Mussar, K. J.·Meng, D. W.·Chen, J. L.·Lahn, B. T.

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Abstract

Plasmids are indispensable in life sciences research and therapeutics development. Currently, most labs custom-build their plasmids. As yet, no systematic data on the quality of lab-made plasmids exist. Here, we report a broad survey of plasmids from hundreds of academic and industrial labs worldwide. We show that nearly half of them contained design and/or sequence errors. For transfer plasmids used in making AAV vectors, which are widely used in gene therapy, about 40% carried mutations in the inverted terminal repeat (ITR) regions due to their inherent instability, which is influenced by flanking GC content. We also list genes difficult to clone into plasmid or package into virus due to their toxicity. Our finding raises serious concerns over the trustworthiness of lab-made plasmids, which parallels the underappreciated mycoplasma contamination and misidentified mammalian cell lines reported previously, and highlights the need for community-wide standards to uphold the quality of this ubiquitous reagent in research and medicine. Accordingly, we propose the concept of good vector practice (GVP) that covers the proper design, construction, in-process QC, final QC, banking and management of plasmids in research and medicine to uphold their quality.

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Bai, X., Hong, J. F., Yu, S., Hu, D. Y., Chen, A. Y., Rich, C. A., Shi, S. J., Xu, S. Y., Croucher, D. M., Mussar, K. J., Meng, D. W., Chen, J. L., Lahn, B. T.. 2024-06-18. Prevalence of errors in lab-made plasmids across the globe. https://doi.org/10.1101/2024.06.17.596931

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