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

Author

Listed:
  • Jennifer A. Byrne

    (New South Wales Health Statewide Biobank, New South Wales Health Pathology
    The University of Sydney)

  • Yasunori Park

    (The University of Sydney)

  • Rachael A. West

    (The University of Sydney
    Kids Research, The Children’s Hospital At Westmead)

  • Amanda Capes-Davis

    (The University of Sydney
    CellBank Australia, Children’s Medical Research Institute)

  • Bertrand Favier

    (University Grenoble Alpes, Team GREPI, Etablissement Français du Sang)

  • Guillaume Cabanac

    (University of Toulouse)

  • Cyril Labbé

    (University Grenoble Alpes, CNRS, Grenoble INP, LIG)

Abstract

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.

Suggested Citation

  • Jennifer A. Byrne & Yasunori Park & Rachael A. West & Amanda Capes-Davis & Bertrand Favier & Guillaume Cabanac & Cyril Labbé, 2021. "The thin ret(raction) line: biomedical journal responses to incorrect non-targeting nucleotide sequence reagents in human gene knockdown publications," Scientometrics, Springer;Akadémiai Kiadó, vol. 126(4), pages 3513-3534, April.
  • Handle: RePEc:spr:scient:v:126:y:2021:i:4:d:10.1007_s11192-021-03871-9
    DOI: 10.1007/s11192-021-03871-9
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    References listed on IDEAS

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    1. Jonathan Knight, 2001. "When the chips are down," Nature, Nature, vol. 410(6831), pages 860-861, April.
    2. Cyril Labbé & Guillaume Cabanac & Rachael A. West & Thierry Gautier & Bertrand Favier & Jennifer A. Byrne, 2020. "Flagging incorrect nucleotide sequence reagents in biomedical papers: To what extent does the leading publication format impede automatic error detection?," Scientometrics, Springer;Akadémiai Kiadó, vol. 124(2), pages 1139-1156, August.
    3. David B. Allison & Andrew W. Brown & Brandon J. George & Kathryn A. Kaiser, 2016. "Reproducibility: A tragedy of errors," Nature, Nature, vol. 530(7588), pages 27-29, February.
    4. Jennifer A. Byrne & Cyril Labbé, 2017. "Striking similarities between publications from China describing single gene knockdown experiments in human cancer cell lines," Scientometrics, Springer;Akadémiai Kiadó, vol. 110(3), pages 1471-1493, March.
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    Cited by:

    1. Sida Feng & Lingzi Feng & Fang Han & Ye Zhang & Yanqing Ren & Lixue Wang & Junpeng Yuan, 2024. "Citation network analysis of retractions in molecular biology field," Scientometrics, Springer;Akadémiai Kiadó, vol. 129(8), pages 4795-4817, August.

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