August 17, 2022

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Nature: Errors in the DNA or RNA sequence of the experimental reagents

Nature Warning: There are errors in the DNA or RNA sequence of the experimental reagents for more than 700 studies

Nature: Errors in the DNA or RNA sequence of the experimental reagents.  A computer analysis study of nearly 12,000 human genetics papers found that the DNA or RNA sequence of the experimental reagents in more than 700 studies had errors.

The team led by cancer researcher Jennifer Byrn at the University of Sydney in Australia pointed out that this is a “worrying issue” because it shows that some of the research on human genes is unreliable and worrying.

These errors may be accidental, but researchers also suspect that there may be academic misconduct.

Since 2015, Byrn has been studying errors in genetics research, when she discovered the problem in five papers reporting a common experiment: using a small piece of DNA to inactivate a gene in cancer cells.

These studies reported the wrong nucleotide sequence in the experiments they conducted. This is not the only problem with these papers. The paper also uses similar language and data. Byrn suspects the products of their paper producers. Currently four papers have been returned.

Byrn continues to search for papers with similar errors. By 2017, she worked with Cyril Labbé, a computer scientist at the University of Grenoble in France, to develop a software called Seek & Blastn that can flag potential errors.

It extracts short nucleotide sequences from papers and compares them with the public nucleotide database Blastn to check whether they match the human genes that should be targeted. Researchers also manually check for mismatches in each tag.

To measure the severity of this problem, the research team screened two journals that they knew had previously published flawed papers: Gene (the research team checked all 7,400 original papers published from 2007 to 2018) and Oncology Reports (2014 All 3,800 open access papers published between 2018 and 2018).

After manual inspection, about 12% of the papers checked by Oncology Reports had errors.

Targeted search

Byrne and her team also pointed to three sub-fields of cancer genetics, where they had previously found problems: papers on the role of specific types of microRNAs in cancer cells; reports on cisplatin or gemcitabine in the treatment of cancer cells or cancer patients The papers; there are also some papers reporting the elimination of the activity of any of the 17 genes to determine their function in cancer cells.

The research team found that more than 25% of about 600 papers in these subfields contained nucleotide sequence errors.

Nature: Errors in the DNA or RNA sequence of the experimental reagents
Jennifer Byrn

The researchers stated in a preprint published on bioRxiv on July 31 that a total of 712 papers—about 6% of the total screened—have errors in the sequence of their nucleotide reagents. These studies have been published in 78 journals and have been cited more than 17,000 times in total. (29 of these studies were published on Springer Nature, and Nature said it would investigate related papers). Of the 712 studies, only 11 were withdrawn, and 3 expressed concerns. Byrne said her team has now emailed editors of all relevant journals or publishers, and they can find contact information, and some people responded that they will investigate these papers.

Oncology Reports editor-in-chief and virologist Demetrios Spandidos told Nature that Byrne had contacted him, but there was not enough time to evaluate all the data described in the manuscript. Molecular biologist Andre Van Wijnen, editor-in-chief of Gene magazine, did not respond.

Unintentional error?

Byrne said that some problems may be unintentional errors. However, she said that researchers have found many unreliable errors, such as the use of polymerase chain reaction to amplify DNA.

The researchers wrote: “We have found that the proportion of nucleotide sequence errors in human gene function papers is unacceptably high. This is a major challenge for the research field aimed at transforming genomics investment into patients.” This wasted. Scientists try to track the time of such research. In the worst case, the paper may be forged and the research may be unreliable.

(source:internet, reference only)

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