A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines
Open accessAbstract
Evidence that some high-impact biomedical results cannot be repeated has stimulated interest in practices that generate findable, accessible, interoperable, and reusable (FAIR) data. Multiple papers have identified specific examples of irreproducibility, but practical ways to make data more reproducible have not been widely studied. Here, five research centers in the NIH LINCS Program Consortium investigate the reproducibility of a prototypical perturbational assay: quantifying the responsiveness of cultured cells to anti-cancer drugs. Such assays are important for drug development, studying cellular networks, and patient stratification. While many experimental and computational factors impact intra- and inter-center reproducibility, the factors most difficult to identify and control are those with a strong dependency on biological context. These factors often vary in magnitude with the drug being analyzed and with growth conditions. We provide ways to identify such context-sensitive factors, thereby improving both the theory and practice of reproducible cell-based assays.
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Although five research centers applied cells and chemicals of the same stock, center-to-center variations up to 200-fold were observed in growth inhibition rates.
“Although the five research centers applied cells and chemicals of the same stock, astonishing center-to-center variations up to 200-fold were observed in growth inhibition rates.”
From In Vitro research Reproducibility: Keeping up High Standards (2019) · cites this paper as Niepel et al., 2019
The Introduction and Results (‘Measuring Drug Responses in Collaboration’) say that five centers received identical cell aliquots and drug stocks, and that initial inter-center variability reached 200-fold. The 200-fold figure refers specifically to GR50 values, a measure of drug potency, not to growth inhibition rates themselves. (LLM, conf=0.86)
Experimental — accuracy not yet measuredATP levels do not necessarily directly correlate to the number of viable cells, resulting in identical EC50 values for some drugs but differing greatly for others.
“ATP levels do not necessarily directly correlate to the number of viable cells, resulting in identical EC50 values for some drugs, but differing greatly for others.”
From In Vitro research Reproducibility: Keeping up High Standards (2019) · cites this paper as Niepel et al., 2019
The Results (Technical Drivers of Variability; page not provided) say ATP-based measurements can diverge from viable-cell counts, with the extent depending on the drug and cell line. The paper reports small differences for some drugs and large differences in GRmax for others, but it does not establish identical or greatly differing EC50 values; for two drugs, GR50 could not be determined from the ATP-assay data. (LLM, conf=0.88)
Experimental — accuracy not yet measuredThe finding of significant interlaboratory variability is consistent with previous attempts to replicate identical protocols across multiple sites for animal and cell line studies.
“The finding of significant interlaboratory variability is also consistent with previous attempts to replicate identical protocols across multiple sites for animal (Crabbe et al., 1999) and cell line studies (Elliott et al., 2017;Niepel et al., 2019).”
From Estimating the replicability of Brazilian biomedical science (2025) · cites this paper as Niepel et al., 2019
Cell seeding, i.e., slight variations in initial cell numbers, was identified as one key source of these variations.
“Cell seeding, i.e. slight variations in initial cell numbers, was identified as one key source of these variations (for more details see Recommendation 5) (Cell density and medium change).”
From In Vitro research Reproducibility: Keeping up High Standards (2019) · cites this paper as Niepel et al., 2019
The subtle interplay between experimental methods and a vast array of poorly defined sources of biological variability was found to be the main cause of the observed irreproducibility.
“Overall, the subtle interplay between experimental methods and a vast array of poorly defined sources of biological variability was found to be the main cause of the observed irreproducibility.”
From In Vitro research Reproducibility: Keeping up High Standards (2019) · cites this paper as Niepel et al., 2019
Niepel and colleagues concluded that most examples of irreproducibility are themselves irreproducible.
“As a consequence of the huge number of individual biological factors involved, Niepel and colleagues came to the rather discouraging conclusion that “most examples of irreproducibility are themselves irreproducible” (Niepel et al., 2019).”
From In Vitro research Reproducibility: Keeping up High Standards (2019) · cites this paper as Niepel et al., 2019
Niepel et al. 2019 systematically addressed inter- and intra-study center variations and identified factors contributing to insufficient reproducibility.
“A recent evocative study of the mammary epithelial cell line MCF10A and growth rate inhibition by anti-cancer drugs systematically addressed inter- and intra-study center variations and identified factors contributing to insufficient reproducibility (Niepel et al., 2019).”
From In Vitro research Reproducibility: Keeping up High Standards (2019) · cites this paper as Niepel et al., 2019
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Percentages, sums and reported differences re-computed from the paper’s own numbers.
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Cites
The FAIR Guiding Principles for scientific data management and stewardship
Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., da Silva Santos, L. B., Bourne, P. E., et al. (2016) · Scientific Data · doi:10.1038/sdata.2016.18 · Cited by 18,423 · see citing works
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
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Self-citationRaise standards for preclinical cancer research
Begley, C. G., & Ellis, L. M. (2012) · Nature · doi:10.1038/483531a · Cited by 2,979 · cited 2× · see citing works
“Adoption of FAIR approaches also responds to concerns from industrial and academic groups about the reproducibility and utility of biomedical research (Arrowsmith, 2011; Baker, 2016; Begley and Ellis, 2012; Prinz et al., 2011) and the adequacy of data-reporting standards (Errington et al.”
BackgroundSystematic identification of genomic markers of drug sensitivity in cancer cells
Garnett, M. J., Edelman, E. J., Heidorn, S. J., Greenman, C. D., Dastur, A., Lau, K. W., Greninger, P., Thompson, I. R., Luo, X., Soares, J., et al. (2012) · Nature · doi:10.1038/nature11005 · Cited by 2,456 · see citing works
Believe it or not: how much can we rely on published data on potential drug targets?
Prinz, F., Schlange, T., & Asadullah, K. (2011) · Nature Reviews Drug Discovery · doi:10.1038/nrd3439-c1 · Cited by 1,888 · see citing works
Widespread potential for growth-factor-driven resistance to anticancer kinase inhibitors
Wilson, T. R., Fridlyand, J., Yan, Y., Penuel, E., Burton, L., Chan, E., Peng, J., Lin, E., Wang, Y., Sosman, J., et al. (2012) · Nature · doi:10.1038/nature11249 · Cited by 1,134 · see citing works
Arrowsmith, J. (2011) · Nature Reviews Drug Discovery · doi:10.1038/nrd3439 · Cited by 622 · see citing works
Inconsistency in large pharmacogenomic studies
Haibe-Kains, B., El-Hachem, N., Birkbak, N. J., Jin, A. C., Beck, A. H., Aerts, H. J. W. L., & Quackenbush, J. (2013) · Nature · doi:10.1038/nature12831 · Cited by 499 · see citing works
Pharmacogenomic agreement between two cancer cell line data sets
The Cancer Cell Line Encyclopedia Consortium, & The Genomics of Drug Sensitivity in Cancer Consortium (2015) · Nature · doi:10.1038/nature15736 · Cited by 418 · see citing works
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“The finding of significant interlaboratory variability is also consistent with previous attempts to replicate identical protocols across multiple sites for animal (Crabbe et al., 1999) and cell line studies (Elliott et al., 2017; Niepel et al., 2019).”
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- Authors
- Niepel, M., Hafner, M., Mills, C. E., Subramanian, K., Williams, E. H., Chung, M., Gaudio, B., Barrette, A. M., Stern, A. D., Hu, B., Korkola, J. E., Gray, J. W., Birtwistle, M. R., Heiser, L. M., Sorger, P. K., Shamu, C. E., Jayaraman, G., Azeloglu, E. U., Iyengar, R., Sobie, E. A., Mills, G. B., Liby, T., Jaffe, J. D., Alimova, M., Davison, D., Lu, X., Golub, T. R., Subramanian, A., Shelley, B., Svendsen, C. N., Ma’ayan, A., Medvedovic, M., Feiler, H. S., Smith, R., & Devlin, K.
- Affiliations
- Harvard University (US)
- Icahn School of Medicine at Mount Sinai (US)
- Oregon Health & Science University (US)
- Corresponding author
- Birtwistle, Marc R.
- Heiser, Laura M.
- Sorger, Peter K.
- ORCID
- Niepel, Mario
- Hafner, Marc
- Mills, Caitlin E.
- Subramanian, Kartik
- Williams, Elizabeth H.
- Chung, Mirra
- Gaudio, Benjamin
- Barrette, Anne Marie
- Stern, Alan D.
- Hu, Bin
- Korkola, James E.
- Gray, Joe W.
- Birtwistle, Marc R.
- Heiser, Laura M.
- Sorger, Peter K.
- Shamu, Caroline E.
- Azeloglu, Evren U.
- Iyengar, Ravi
- Sobie, Eric A.
- Mills, Gordon B.
- Liby, Tiera
- Jaffe, Jacob D.
- Golub, Todd R.
- Subramanian, Aravind
- Svendsen, Clive N.
- Ma’ayan, Avi
- Medvedovic, Mario
- Feiler, Heidi S.
- Smith, Rebecca
- Devlin, Kaylyn
- Venue
- Cell Systems
- Publisher
- Elsevier BV
- Published
- 2019-07
- Volume
- 9
- Issue
- 1
- Pages
- 35-48.e5
- ISSN
- 2405-4712 (ISSN-L)
- PMC
- PMC6700527
- OpenAlex
- W2959521790
- Cited by
- 133
- References
- 9
- Citations by year
- 2026: 16 · 2025: 19 · 2024: 8 · 2023: 19 · 2022: 32 · 2021: 18 · 2020: 18 · 2019: 3
- FWCI
- 21.01
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cell Systems (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion, cc-by)
- Funders
- Thermo Fisher
- Micron,
- PDX Pharmaceuticals
- Susan G. Komen Foundation
- Prospect Creek Foundation
- NCI
- NIH
- AztraZeneca
- Karus Therapeutics
- Nanostring
- Pfizer
- Tesaro
- Adelson Medical Research Foundation
- Breast Cancer Research Foundation
- Komen Research Foundation
- Ovarian Cancer Research Foundation
- Topics
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Health Sciences › Veterinary › Small Animals › Animal testing and alternatives
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- reproducibility, mammalian cell lines, anticancer agents, FAIR data, cell-based drug screening, patient stratification
- MeSH terms
- Drug Development, Animals, Antineoplastic Agents, Humans, Mammals, Neoplasms, Reproducibility of Results, Observer Variation, Cell Culture Techniques, Computational Biology, Cell Line, Tumor, High-Throughput Screening Assays
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