Incorrect primer sequences in the article on methylprednisolone treatment

Tamm, Andres

doi:10.1111/ane.12507

Cited by 5 publications

(5 citation statements)

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“…Although there have been previous reports of wrongly identified PCR primers and gene knockdown reagents in single articles or small cohorts ( 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 21 ), the present study is the first to systematically fact-check the identities of nucleotide sequences in more than 3,400 research articles. Our supported application of S&B ( 12 , 27 ) ( https://www.protocols.io/view/seek-amp-blastn-standard-operating-procedure-bjhpkj5n ) to screen three targeted corpora and two journals identified 712 articles published across 78 journals that described more than 1,500 wrongly identified sequences.…”

Section: Discussionmentioning

confidence: 85%

“…However, as nucleotide sequences cannot be understood by eye, we have proposed that nucleotide sequence reagents are susceptible to different types of errors ( 8 , 11 , 12 ). These error types represent the equivalent of spelling errors ( 12 , 14 , 15 ), as well as identity errors, where a correct sequence is replaced by a different and possibly genetically unrelated sequence ( 11 , 12 , 13 , 16 , 17 , 18 , 19 , 20 , 21 ).…”

Section: Introductionmentioning

confidence: 99%

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Identification of human gene research articles with wrongly identified nucleotide sequences

et al. 2022

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Nucleotide sequence reagents underpin molecular techniques that have been applied across hundreds of thousands of publications. We have previously reported wrongly identified nucleotide sequence reagents in human research publications and described a semi-automated screening tool Seek & Blastn to fact-check their claimed status. We applied Seek & Blastn to screen >11,700 publications across five literature corpora, including all original publications in Gene from 2007 to 2018 and all original open-access publications in Oncology Reports from 2014 to 2018. After manually checking Seek & Blastn outputs for >3,400 human research articles, we identified 712 articles across 78 journals that described at least one wrongly identified nucleotide sequence. Verifying the claimed identities of >13,700 sequences highlighted 1,535 wrongly identified sequences, most of which were claimed targeting reagents for the analysis of 365 human protein-coding genes and 120 non-coding RNAs. The 712 problematic articles have received >17,000 citations, including citations by human clinical trials. Given our estimate that approximately one-quarter of problematic articles may misinform the future development of human therapies, urgent measures are required to address unreliable gene research articles.

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Section: Discussionmentioning

confidence: 85%

Section: Introductionmentioning

confidence: 99%

Identification of human gene research articles with wrongly identified nucleotide sequences

et al. 2022

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“…Because written DNA or RNA sequences lack obvious meaning, even short nucleotide sequences are susceptible to being transcribed incorrectly (Byrne et al 2019;Labbé et al 2019). Nucleotide sequences can incorporate the equivalent of spelling mistakes (Chiarella et al 2015;Habbal et al 2005;Labbé et al 2019;Shannon et al 2008) and intended nucleotide sequences can also be substituted by nucleotide sequences with entirely different identities and meanings (Byrne and Labbé 2017;Chiarella et al 2015;Katavetin et al 2005;Kocemba et al 2016;Labbé et al 2019;Tamm 2016). Whereas typographic errors within nucleotide sequence reagents can have variable significance, wrongly identified nucleotide sequence reagents will almost certainly invalidate any experiment that uses such reagents (Byrne et al 2019;Labbé et al 2019).…”

Section: Published Nucleotide Sequence Reagent Errorsmentioning

confidence: 99%

The thin ret(raction) line: biomedical journal responses to incorrect non-targeting nucleotide sequence reagents in human gene knockdown publications

Byrne¹,

Park²,

West³

et al. 2021

Scientometrics

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The capacity of the scientific literature to self-correct is of vital importance, but few studies have compared post-publication journal responses to specific error types. We have compared journal responses to a specific reagent error in 31 human gene knockdown publications, namely a non-targeting or negative control nucleotide sequence that is instead predicted to target a human gene. The 31 papers published by 13 biomedical journals generated 26 published responses (14 retractions, 5 expressions of concern, 7 author corrections which included one resolved expression of concern) as well as 6 stated decisions to take no action. Variations in published responses were noted both between journals and by 4 journals that published different responses to at least 2 papers. A subset of published responses revealed conflicting explanations for the wrongly identified control reagent, despite 30/31 papers obtaining their gene knockdown reagents from the same external supplier. Viewed collectively, different journal responses to human gene knockdown publications with a common reagent error type suggest that editorial staff require more support to interpret post-publication notifications of incorrect nucleotide sequence reagents. We propose a draft template to facilitate the communication, interpretation and investigation of published errors, including errors affecting research reagents.

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“…In addition to problems of antibody cross-reactivity and variable performance (2), ELISA kits have been found to include antibodies that detect different targets from those claimed (3,4). Independent studies have described research papers where the identities of some nucleotide sequence reagents do not match their descriptions (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17), including oligonucleotide probes on microarrays (18,19), and shRNAs in libraries (20). Finally, due to cross-contamination and/or uncertainty over donor origins, many human cell lines are known to be wrongly identified (21)(22)(23)(24)(25).…”

Section: Introduction (N=4992 Words)mentioning

confidence: 99%

Misspellings or “miscellings”-non-verifiable cell lines in cancer research publications

Oste,

Pathmendra,

Richardson

et al. 2024

Preprint

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Reproducible laboratory research relies on correctly identified reagents. We have previously described human gene research papers with wrongly identified nucleotide sequence reagent(s), including papers studying miR-145. Manually verifying reagent identities in more recent miR-145 papers found 20/36 (56%) and 6/36 (17%) miR-145 papers with misidentified nucleotide sequence reagent(s) and human cell line(s), respectively. We also found 5 cell line identifiers in two miR-145 papers with wrongly identified nucleotide sequences and cell lines, and 18 identifiers published elsewhere that did not correspond to indexed cell lines. These cell line identifiers were described as non-verifiable, as their identities appeared uncertain. Studying 420 papers that mentioned 8 different non-verifiable cell line identifier(s) found 235 papers (56%) that appeared to refer to BGC-803, BSG-803, BSG-823, GSE-1, HGC-7901, HGC-803 and/or MGC-823 as independent cell lines. We could not find publications describing how these cell lines were established, and they were not indexed in claimed externally accessible cell line repositories. While some papers stated that STR profiles had been generated for BGC-803, GSE-1 and/or MGC-823 cells, no STR profiles were identified. In summary, non-verifiable human cell lines represent new challenges to research reproducibility and require further investigation to clarify their identities.

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Incorrect primer sequences in the article on methylprednisolone treatment

Cited by 5 publications

References 5 publications

Identification of human gene research articles with wrongly identified nucleotide sequences

Identification of human gene research articles with wrongly identified nucleotide sequences

The thin ret(raction) line: biomedical journal responses to incorrect non-targeting nucleotide sequence reagents in human gene knockdown publications

Misspellings or “miscellings”-non-verifiable cell lines in cancer research publications

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