[HN Gopher] Serious errors plague DNA tool that's a workhorse of...
       ___________________________________________________________________
        
       Serious errors plague DNA tool that's a workhorse of biology
        
       Author : bookofjoe
       Score  : 81 points
       Date   : 2024-07-11 11:44 UTC (11 hours ago)
        
 (HTM) web link (www.nature.com)
 (TXT) w3m dump (www.nature.com)
        
       | vikramkr wrote:
       | This is good important work - similar to the stuff about
       | antibodies that's been looked into. Hopefully as lab
       | automation/analysis costs keep coming down it'll become more and
       | more feasible to implement validation/characterization
       | requirements into publication processes and increase
       | reproducibility, and it'll be important to know where we're
       | falling short currently.
        
       | the__alchemist wrote:
       | I've been learning a lot about molecular biology recently, and am
       | about to run some procedures related to plasmid isolation, gene
       | cloning, and expression. Of note, the resources I've read, from
       | AddGene, and The Bumbling Biochemist (excellent Youtube channel)
       | emphasize sending your plasmids in for sequencing once complete,
       | due to all the errors that can occur.
       | 
       | 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.
        
         | throwup238 wrote:
         | I figure the vast majority of plasmids are used for mundane
         | stuff like GFP expression. Not really worth sending in for an
         | analysis because everyone just redoes the experiment if it
         | fails to express anyway.
        
         | kylebenzle wrote:
         | Exactly! Everyone worth their salt sequences before, after and
         | during insertion and expression.
         | 
         | I read this article expecting something new but it's just
         | reporting that some people are lazy and do bad science.
         | 
         | This article is nonsense.
        
         | Feuilles_Mortes wrote:
         | Before these companies like plasmidsaurus that do whole-plasmid
         | sequencing for relatively cheap with nanopore, people generally
         | only sequenced a region of interest using sanger sequencing.
         | The rest of the plasmid was assumed to be mostly correct, as
         | long as it grows on a bacterial resistance. As noted in the
         | article, the rise of nanopore-based whole-plasmid sequencing
         | has reduced a lot of these types of errors.
        
           | the__alchemist wrote:
           | OK, this looks great. $15-60 for plasmid sampling!
        
       | HayBale wrote:
       | Honestly, a crazy amount of biology and bioinfo works like that.
       | Do any in silico analysis on NCBI accession genomes. I would say
       | wast majority of them is either shoddy at best and at worst
       | completely mislabeled.
       | 
       | 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.
        
         | dsign wrote:
         | You are onto something there. I believe that there is a lot of
         | good science being made. But there is a world of difference
         | between even a well-conducted research paper and a 99.999999%
         | SLA: we don't have anything like that in biotech. Some will say
         | that you just can't. I say that we are not trying hard enough.
         | 
         | Back in the day I did some PhD research in horizontal gene
         | transfer with plasmids. Really fascinating stuff.
        
       | protomolecule wrote:
       | I wonder to what degree this affects DNA forensics tools.
        
       | cyanydeez wrote:
       | Evolution used "it's not a bug, it's a feature" and it's super
       | effective.
        
       ___________________________________________________________________
       (page generated 2024-07-11 23:01 UTC)