Newswise — Chicago, IL - June 24, 2024 - 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:
VectorBuilder is a global leader in gene delivery technologies. As a trusted partner for thousands of labs and biotech/pharma companies across the globe, VectorBuilder offers a full spectrum of gene delivery solutions covering virtually all research and clinical needs from bench to bedside.
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