Serious errors plague DNA tool that's a workhorse of biology
Nearly half of lab-made plasmids in biology contain design flaws, impacting gene expression. Lack of quality control raises reproducibility concerns. Sequencing and sharing plasmid sequences are recommended to prevent errors.
Read original articleResearchers have found that nearly half of the laboratory-made plasmids used in biology have design flaws, including errors in sequences crucial for expressing therapeutic genes. This discovery raises concerns about the reproducibility of experiments. Plasmids are essential tools in biology labs, allowing for the creation of designer plasmids containing genes of interest. The study highlights a lack of knowledge regarding proper quality control on plasmids in labs. Errors in plasmid design can lead to wasted time and resources, as seen in cases where experiments failed due to faulty plasmids. The most common errors found were related to key gene-therapy tools, potentially affecting the effectiveness of treatments. Experts suggest sequencing plasmids to identify errors and emphasize the importance of sharing plasmid sequences in open-access repositories to prevent issues. While some believe that errors are unlikely to cause problems in clinical settings due to stringent regulatory standards, the study underscores the need for researchers to pay closer attention to the quality of these fundamental lab tools.
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I am wondering if the plasmids the researchers here tested simply weren't sequenced. This wouldn't explain all classes of errors (like toxic protein production), but it may explain some. When you order from AddGene, they provide both the depositor's sequence results, if available, and their own results. The paper doesn't mention AddGene specifically; I'm curious how their plasmids compare to the ones tested.
Regarding toxic proteins: It seems like that would be a straightforward software addition to pass sequencing results through.
Bioinfo tools? You scrape the surface of the reported results and see what is inside and a lot of stuff is either broken or work on a trust me bro principle.
Sequencing? In one technology results can be a bit different depending on the graphic card used and reported error rate is kinda shady.
Don't get me wrong people working with these stuff are amazing but the constant push for publishing more and more and the profit drive of the companies does a lot of bad stuff.
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