Utility of Checklist to Describe Experimental Methods for Investigating Molecular Biomarkers
Abstract
INTRODUCTION: In research articles, detailed description of experimental methods and reagents is fundamental for correct reproducibility of the published data. This becomes even more important when such data contribute to identify molecular targets and toxicity biomarkers whose role is crucial in the physiology and pathology of human health. Methods & Objectives: To achieve good reproducibility of data we took advantage of others' experiences and analyzed molecular biology and immunodetection techniques in 32 journal articles investigating the human NRF2 and Keap1 genes involved in the cell response to oxidative stress. RESULTS & CONCLUSIONS: In conclusion of the analysis, we assessed deficiency of information in the published methods, making it difficult to select appropriate protocols. Underlining the importance of assay reproducibility, this paper proposes the utility of a minimum information checklist of methods for biomarker detection.
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Independent studies have reported that the identities of some nucleotide sequence reagents do not match their descriptions.
“Independent studies have described examples where the identities of some nucleotide sequence reagents do not match their descriptions (5–17), including oligonucleotide probes on microarrays (18, 19), and shRNAs in libraries (20).”
From Misspellings or “miscellings”—Non‐verifiable and unknown cell lines in cancer research publications (2024) · cites this paper as [7]
Many studies indicate that experimental reagents can be wrongly identified in publications.
“many studies now indicate that experimental reagents can be wrongly identified in publications”
From Misspellings or “miscellings”—Non‐verifiable and unknown cell lines in cancer research publications (2024) · cites this paper as [7]
Wrongly identified reagents can cause failed attempts to reproduce published results.
“These wrongly identified reagents can produce a range of downstream consequences, including failed attempts to reproduce published results (3, 5, 7, 11, 16), and potentially incorrect interpretations of preclinical data leading to misdirected translational research (10, 12, 25).”
From Misspellings or “miscellings”—Non‐verifiable and unknown cell lines in cancer research publications (2024) · cites this paper as [7]
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Flagged first, then by citations
Cited by
Sorted by citations
Identification of human gene research articles with wrongly identified nucleotide sequences
Park, Y., West, R. A., Pathmendra, P., Favier, B., Stoeger, T., Capes-Davis, A., Cabanac, G., Labbé, C., & Byrne, J. A. (2022) · Life Science Alliance · doi:10.26508/lsa.202101203 · Cited by 37 · see citing works
“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).”
Byrne, J. A., Park, Y., West, R. A., Capes-Davis, A., Favier, B., Cabanac, G., & Labbé, C. (2021) · Scientometrics · doi:10.1007/s11192-021-03871-9 · Cited by 21 · see citing works
Meng, M. (2017) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2017.07.001 · Cited by 24 · see citing works
“Plants containing a large amount of digitoflavone have been applied in Chinese traditional medicine for a long time to treat inflammatory diseases, hypertension, and cancer [16,17].”
BackgroundMisspellings or “miscellings”—Non‐verifiable and unknown cell lines in cancer research publications
Oste, D. J., Pathmendra, P., Richardson, R. A. K., Johnson, G., Ao, Y., Arya, M. D., Enochs, N. R., Hussein, M., Kang, J., Lee, A., et al. (2024) · International Journal of Cancer · doi:10.1002/ijc.34995 · Cited by 18 · see citing works
“20 25 These wrongly identified reagents can produce a range of downstream consequences, including failed attempts to reproduce published results, 3,5,7,11,16 and potentially incorrect interpretations of preclinical data leading to misdirected translational research.”
Pathmendra, P., Park, Y., Enguita, F. J., & Byrne, J. A. (2024) · Naunyn-Schmiedeberg s Archives of Pharmacology · doi:10.1007/s00210-023-02846-2 · Cited by 13 · see citing works
- Authors
- Chiarella, P., Carbonari, D., & Iavicoli, S.
- Affiliations
- Istituto Nazionale per l'Assicurazione Contro gli Infortuni sul Lavoro (IT)
- Venue
- Biomarkers in Medicine
- Publisher
- Informa UK Limited
- Published
- 2015-10
- Volume
- 9
- Issue
- 10
- Pages
- 989-995
- ISSN
- 1752-0363 (ISSN-L)
- 1752-0371
- OpenAlex
- W2141121359
- Cited by
- 5
- References
- 43
- Citations by year
- 2024: 2 · 2022: 1 · 2021: 1 · 2017: 1
- FWCI
- 0.14
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Biomarkers in Medicine (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics, phytochemicals, and oxidative stress
- Social Sciences › Arts and Humanities › History and Philosophy of Science › Academic Writing and Publishing
- Social Sciences › Decision Sciences › Statistics, Probability and Uncertainty › Meta-analysis and systematic reviews
- Keywords
- molecular biomarkers, reproducibility, Nrf2, Keap1, oxidative stress, immunological detection, molecular biology techniques, biomarkers of toxicity
- MeSH terms
- Kelch-Like ECH-Associated Protein 1, Humans, Immunoassay, Biomarkers, Oxidative Stress, Computational Biology, Reverse Transcriptase Polymerase Chain Reaction, Intracellular Signaling Peptides and Proteins, NF-E2-Related Factor 2, Checklist
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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