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Pathmendra P, Park Y, Enguita FJ, Byrne JA. Verification of nucleotide sequence reagent identities in original publications in high impact factor cancer research journals. Naunyn Schmiedebergs Arch Pharmacol 2024:10.1007/s00210-023-02846-2. [PMID: 38194106 DOI: 10.1007/s00210-023-02846-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 01/10/2024]
Abstract
Human gene research studies that describe wrongly identified nucleotide sequence reagents have been mostly identified in journals of low to moderate impact factor, where unreliable findings could be considered to have limited influence on future research. This study examined whether papers describing wrongly identified nucleotide sequences are also published in high-impact-factor cancer research journals. We manually verified nucleotide sequence identities in original Molecular Cancer articles published in 2014, 2016, 2018, and 2020, including nucleotide sequence reagents that were claimed to target circRNAs. Using keywords identified in some 2018 and 2020 Molecular Cancer papers, we also verified nucleotide sequence identities in 2020 Oncogene papers that studied miRNA(s) and/or circRNA(s). Overall, 3.8% (251/6647) and 4.0% (47/1165) nucleotide sequences that were verified in Molecular Cancer and Oncogene papers, respectively, were found to be wrongly identified. Wrongly identified nucleotide sequences were distributed across 18% (91/500) original Molecular Cancer papers, including 38% (31/82) Molecular Cancer papers from 2020, and 40% (21/52) selected Oncogene papers from 2020. Original papers with wrongly identified nucleotide sequences were therefore unexpectedly frequent in two high-impact-factor cancer research journals, highlighting the risks of employing journal impact factors or citations as proxies for research quality.
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Affiliation(s)
- Pranujan Pathmendra
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Yasunori Park
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisbon, Portugal
| | - Jennifer A Byrne
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia.
- NSW Health Statewide Biobank, NSW Health Pathology, Camperdown, NSW, 2050, Australia.
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Byrne JA, Park Y, Richardson RAK, Pathmendra P, Sun M, Stoeger T. Protection of the human gene research literature from contract cheating organizations known as research paper mills. Nucleic Acids Res 2022; 50:12058-12070. [PMID: 36477580 PMCID: PMC9757046 DOI: 10.1093/nar/gkac1139] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Human gene research generates new biology insights with translational potential, yet few studies have considered the health of the human gene literature. The accessibility of human genes for targeted research, combined with unreasonable publication pressures and recent developments in scholarly publishing, may have created a market for low-quality or fraudulent human gene research articles, including articles produced by contract cheating organizations known as paper mills. This review summarises the evidence that paper mills contribute to the human gene research literature at scale and outlines why targeted gene research may be particularly vulnerable to systematic research fraud. To raise awareness of targeted gene research from paper mills, we highlight features of problematic manuscripts and publications that can be detected by gene researchers and/or journal staff. As improved awareness and detection could drive the further evolution of paper mill-supported publications, we also propose changes to academic publishing to more effectively deter and correct problematic publications at scale. In summary, the threat of paper mill-supported gene research highlights the need for all researchers to approach the literature with a more critical mindset, and demand publications that are underpinned by plausible research justifications, rigorous experiments and fully transparent reporting.
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Affiliation(s)
- Jennifer A Byrne
- To whom correspondence should be addressed. Tel: +61 2 4920 4135;
| | - Yasunori Park
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
| | - Reese A K Richardson
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, USA
| | - Pranujan Pathmendra
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
| | - Mengyi Sun
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, USA
| | - Thomas Stoeger
- To whom correspondence should be addressed. Tel: +61 2 4920 4135;
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Parker L, Boughton S, Lawrence R, Bero L. Experts identified warning signs of fraudulent research: a qualitative study to inform a screening tool. J Clin Epidemiol 2022; 151:1-17. [PMID: 35850426 DOI: 10.1016/j.jclinepi.2022.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/24/2022] [Accepted: 07/11/2022] [Indexed: 12/25/2022]
Abstract
OBJECTIVE Fraudulent research exists but can be difficult to spot. Made-up studies and results can affect systematic reviews and clinical guidelines, causing harm through incorrect treatments and practices. Our aim was to explore indicators of research fraud that could be included in a screening tool to identify potentially problematic studies warranting a closer scrutiny. STUDY DESIGN AND SETTING We conducted a qualitative international interview study, purposively recruiting participants with experience and/or expertise in research integrity, systematic reviews, biomedical publishing, or whistle-blowing research fraud. We used a thematic analysis to identify major concepts and ideas. RESULTS We contacted 49 potential participants and interviewed 30 from 12 countries. Participants described research fraud as a growing concern, with a lack of widely accessible resources or education to assist in flagging problematic studies. They discussed early warning signs that could be contained in a screening tool for use either prepublication or postpublication. We did not speak to participants from indexing services, information software/analytics companies, or the public. Our suggested screening tools are empirically derived but are preliminary and not validated. CONCLUSION A practical tool of early warning signs for research fraud would be useful for peer reviewers, editors, publishers, and systematic reviewers.
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Affiliation(s)
- Lisa Parker
- School of Pharmacy, Charles Perkins Centre, The University of Sydney, New South Wales, Australia
| | | | - Rosa Lawrence
- Center for Bioethics and Humanities, University of Colorado Anschutz Medical Campus, CO, USA
| | - Lisa Bero
- Center for Bioethics and Humanities, University of Colorado Anschutz Medical Campus, CO, USA.
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Teixeira da Silva JA. A Synthesis of the Formats for Correcting Erroneous and Fraudulent Academic Literature, and Associated Challenges. J Gen Philos Sci 2022; 53:583-599. [PMID: 35669840 PMCID: PMC9159037 DOI: 10.1007/s10838-022-09607-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/14/2021] [Accepted: 02/12/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED Academic publishing is undergoing a highly transformative process, and many established rules and value systems that are in place, such as traditional peer review (TPR) and preprints, are facing unprecedented challenges, including as a result of post-publication peer review. The integrity and validity of the academic literature continue to rely naively on blind trust, while TPR and preprints continue to fail to effectively screen out errors, fraud, and misconduct. Imperfect TPR invariably results in imperfect papers that have passed through varying levels of rigor of screening and validation. If errors or misconduct were not detected during TPR's editorial screening, but are detected at the post-publication stage, an opportunity is created to correct the academic record. Currently, the most common forms of correcting the academic literature are errata, corrigenda, expressions of concern, and retractions or withdrawals. Some additional measures to correct the literature have emerged, including manuscript versioning, amendments, partial retractions and retract and replace. Preprints can also be corrected if their version is updated. This paper discusses the risks, benefits and limitations of these forms of correcting the academic literature. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10838-022-09607-4.
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Park Y, West RA, Pathmendra P, Favier B, Stoeger T, Capes-Davis A, Cabanac G, Labbé C, Byrne JA. Identification of human gene research articles with wrongly identified nucleotide sequences. Life Sci Alliance 2022; 5:e202101203. [PMID: 35022248 PMCID: PMC8807875 DOI: 10.26508/lsa.202101203] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 01/01/2023] Open
Abstract
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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Affiliation(s)
- Yasunori Park
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Rachael A West
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, Australia
| | | | - Bertrand Favier
- Université Grenoble Alpes, Translationnelle et Innovation en Médecine et Complexité, Grenoble, France
| | - Thomas Stoeger
- Successful Clinical Response in Pneumonia Therapy Systems Biology Center, Northwestern University, Evanston, IL, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Genetic Medicine, Northwestern University School of Medicine, Chicago, IL, USA
| | - Amanda Capes-Davis
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- CellBank Australia, Children's Medical Research Institute, Westmead, Australia
| | - Guillaume Cabanac
- Computer Science Department, Institut de Recherche en Informatique de Toulouse, Unité Mixte de Recherche 5505 Centre National de la Recherche Scientifique (CNRS), University of Toulouse, Toulouse, France
| | - Cyril Labbé
- Université Grenoble Alpes, CNRS, Grenoble INP, Laboratoire d'Informatique de Grenoble, Grenoble, France
| | - Jennifer A Byrne
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- New South Wales Health Statewide Biobank, New South Wales Health Pathology, Camperdown, Australia
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Teixeira da Silva JA. Issues and challenges to reproducibility of cancer research: a commentary. Future Oncol 2022; 18:1417-1422. [DOI: 10.2217/fon-2021-1378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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