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Oste DJ, Pathmendra P, Richardson RAK, Johnson G, Ao Y, Arya MD, Enochs NR, Hussein M, Kang J, Lee A, Danon JJ, Cabanac G, Labbé C, Davis AC, Stoeger T, Byrne JA. Misspellings or "miscellings"-Non-verifiable and unknown cell lines in cancer research publications. Int J Cancer 2024; 155:1278-1289. [PMID: 38751110 PMCID: PMC11296894 DOI: 10.1002/ijc.34995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/04/2024] [Accepted: 04/18/2024] [Indexed: 06/23/2024]
Abstract
Reproducible laboratory research relies on correctly identified reagents. We have previously described gene research papers with wrongly identified nucleotide sequence(s), including papers studying miR-145. Manually verifying reagent identities in 36 recent miR-145 papers found that 56% and 17% of papers described misidentified nucleotide sequences and cell lines, respectively. We also found 5 cell line identifiers in miR-145 papers with misidentified nucleotide sequences and cell lines, and 18 cell line identifiers published elsewhere, that did not represent indexed human cell lines. These 23 identifiers were described as non-verifiable (NV), as their identities were unclear. Studying 420 papers that mentioned 8 NV identifier(s) found 235 papers (56%) that referred to 7 identifiers (BGC-803, BSG-803, BSG-823, GSE-1, HGC-7901, HGC-803, and MGC-823) as independent cell lines. We could not find any publications describing how these cell lines were established. Six cell lines were sourced from cell line repositories with externally accessible online catalogs, but these cell lines were not indexed as claimed. Some papers also stated that short tandem repeat (STR) profiles had been generated for three cell lines, yet no STR profiles could be identified. In summary, as NV cell lines represent new challenges to research integrity and reproducibility, further investigations are required to clarify their status and identities.
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Affiliation(s)
- Danielle J. Oste
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, NSW, Australia
| | - Pranujan Pathmendra
- 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, IL, USA
| | - Gracen Johnson
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
| | - Yida Ao
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
| | - Maya D. Arya
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
| | - Naomi R. Enochs
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
| | - Muhammed Hussein
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
| | - Jinghan Kang
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
| | - Aaron Lee
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
| | - Jonathan J. Danon
- School of Chemistry, Faculty of Science, The University of Sydney, NSW, Australia
| | - Guillaume Cabanac
- IRIT UMR 5505 CNRS, University of Toulouse, Toulouse, France
- Institut Universitaire de France (IUF), Paris, France
| | - Cyril Labbé
- Université Grenoble Alpes, CNRS, Grenoble INP, Laboratoire d’Informatique de Grenoble, Grenoble, France
| | - Amanda Capes Davis
- CellBank Australia, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Thomas Stoeger
- Feinberg School of Medicine in the Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, IL, USA
- The Potocsnak Longevity Institute, Northwestern University, Chicago, IL, USA
- Simpson Querrey Lung Institute for Translational Science, Chicago, IL, USA
| | - Jennifer A. Byrne
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
- NSW Health Statewide Biobank, NSW Health Pathology, Camperdown, NSW, Australia
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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-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:5049-5066. [PMID: 38194106 PMCID: PMC11166861 DOI: 10.1007/s00210-023-02846-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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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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] [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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The thin ret(raction) line: biomedical journal responses to incorrect non-targeting nucleotide sequence reagents in human gene knockdown publications. Scientometrics 2021. [DOI: 10.1007/s11192-021-03871-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
AbstractThe 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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