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Press Release   |   Jul 01, 2024

High Prevalence of Errors Found in Lab-Made Plasmids Globally: Study Reveals Critical Quality Control Issues

A new study conducted by VectorBuilder, a global leader in plasmid design and gene delivery solutions, has unveiled alarming rates of errors in lab-made plasmids worldwide. The study, titled "Prevalence of errors in lab-made plasmids across the globe," reveals that nearly 50% of plasmids used in life sciences research and therapeutic development contain significant design and sequence errors that could severely impact their functionality.

Study Overview and Key Findings

The study analyzed over 2,500 plasmids submitted to VectorBuilder from both academic and industrial laboratories across different regions, including North America, Europe, and Asia. The comprehensive analysis yielded several critical insights: 

  • Design Errors: Approximately 15% of the plasmids examined had major design flaws. These errors often included incorrect promoter placements, improper coding sequences, and misannotations, which could lead to dysfunctional or misregulated genetic constructs.
  • Sequence Variations: About 35% of plasmids subjected to direct sequencing exhibited sequence discrepancies in functionally important regions compared to their reference sequences. Such variations included point mutations, insertions, deletions, and sequence rearrangements.
  • AAV Transfer Plasmids: Among the AAV (Adeno-Associated Virus) transfer plasmids, which are pivotal reagents in developing gene therapy drugs, nearly 40% showed mutations in their Inverted Terminal Repeat (ITR) regions. The instability of these regions, influenced by the high GC content of flanking sequences, poses significant challenges for gene delivery efficacy.
  • Toxic Genes: The study identified a list of genes that are particularly challenging to clone into plasmids or package into viral vectors due to their inherent toxicity. These genes often lead to low yields or unstable constructs, complicating experimental reproducibility and therapeutic applications.

Implications for Research and Therapeutics

The implications of these findings are profound. As Dr. Bruce Lahn, senior author and Chief Scientific Officer at VectorBuilder, explains, “Our findings raise serious concerns over the trustworthiness of a ubiquitous and foundational reagent in both life sciences research and therapeutic development. The prevalence of design and sequence errors in lab-made plasmids parallels the widespread issues of mycoplasma contamination and misidentified cell lines reported previously. These serious issues went under-the-radar for many years simply because researchers did not think to question their quality, but later became recognized as major problems by the scientific community.”

Lahn further emphasizes the urgency of addressing these issues, stating, “Given the critical role plasmids play in both basic research and medicine, it is imperative that we establish rigorous quality control standards. Our study highlights the need for community-wide efforts to improve the reliability of gene delivery vectors.”

Recommendations for Standardization

The study calls for the implementation of standardized quality controls in plasmid construction, aligning them with other essential quality measures in research and therapeutic applications. Specific recommendations include:

  • Standardized Design Principles: Establishing a set of standardized plasmid design principles for all the major research and therapeutic applications.
  • Best Experimental Practices: Adoption of the best experimental practices in the construction, propagation, storage, transfer and QC of plasmids, as well as related reagents such as libraries and recombinant viruses.
  • Sharing of Expertise: Establishing mechanisms that encourage researchers to share their expertise on plasmids, especially tips for improving vector performance and avoiding pitfalls.
     

About the Authors

The research was spearheaded by Dr. Xingjian Bai at VectorBuilder under the direction of Dr. Bruce T. Lahn, with contributions from a multidisciplinary team including Jack F. Hong, Shan Yu, David Y. Hu, Amy Y. Chen, Constance A. Rich, Silk J. Shi, Sandy Y. Xu, Daniel M. Croucher, Kristofer J. Müssar, Daniel W. Meng, and Jane L. Chen. The team's expertise spans microbiology, genetics, bioinformatics, and clinical research, ensuring a comprehensive and robust analysis. 

Publication Details

Title: Prevalence of errors in lab-made plasmids across the globe

Authors: Xingjian Bai, Jack F. Hong, Shan Yu, David Y. Hu, Amy Y. Chen, Constance A. Rich, Silk J. Shi, Sandy Y. Xu, Daniel M. Croucher, Kristofer J. Müssar, Daniel W. Meng, Jane L. Chen, and Bruce T. Lahn

Journal: bioRxiv

About VectorBuilder Inc.

VectorBuilder is a global leader in gene delivery technologies. As a trusted partner in thousands of labs and biotech/pharma companies around the world, VectorBuilder is a one-stop shop for the design, development and optimization of gene delivery solutions from basic research to clinical applications. Its award-winning Vector Design Studio is a transformative innovation that allows researchers to easily design and order custom vectors online, freeing them from the tedious work of cloning and packaging vectors in the lab. The global company boasts high-throughput vector production capacity, vast vector and component inventories, one-on-one CRO solutions that include advanced AAV capsid engineering capabilities and state-of-the-art GMP facilities. With leading R&D and CDMO manufacturing capacity, the VectorBuilder team strives to provide the most effective gene delivery solutions and develop new tools for life sciences research and genetic medicine.

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