Cited by 133Scientific Computing and Data ManagementAnimal testing and alternativesComputational Drug Discovery Methods

A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines

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Niepel, Mario, Hafner, Marc, Mills, Caitlin E., Subramanian, Kartik, Williams, Elizabeth H., Chung, Mirra, Gaudio, Benjamin, Barrette, Anne Marie +27 more·2019·Cell Systems

Abstract

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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Crossref · 10.1016/j.cels.2019.06.005

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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 measured
  • 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.

    “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 measured
  • The 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

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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.
Venue
Cell Systems
Publisher
Elsevier BV
Published
2019-07
Volume
9
Issue
1
Pages
35-48.e5
ISSN
2405-4712 (ISSN-L)
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
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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