The DOI matches its Crossref record; 23 of the 23 references it cites were found in a registry or an index.
Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium
Open accessAbstract
Standardization of immunophenotyping requires careful attention to reagents, sample handling, instrument setup, and data analysis, and is essential for successful cross-study and cross-center comparison of data. Experts developed five standardized, eight-color panels for identification of major immune cell subsets in peripheral blood. These were produced as pre-configured, lyophilized, reagents in 96-well plates. We present the results of a coordinated analysis of samples across nine laboratories using these panels with standardized operating procedures (SOPs). Manual gating was performed by each site and by a central site. Automated gating algorithms were developed and tested by the FlowCAP consortium. Centralized manual gating can reduce cross-center variability, and we sought to determine whether automated methods could streamline and standardize the analysis. Within-site variability was low in all experiments, but cross-site variability was lower when central analysis was performed in comparison with site-specific analysis. It was also lower for clearly defined cell subsets than those based on dim markers and for rare populations. Automated gating was able to match the performance of central manual analysis for all tested panels, exhibiting little to no bias and comparable variability. Standardized staining, data collection, and automated gating can increase power, reduce variability, and streamline analysis for immunophenotyping.
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Cites
Standardizing immunophenotyping for the Human Immunology Project
Maecker, H. T., McCoy, J. P., & Nussenblatt, R. (2012) · Nature Reviews Immunology · doi:10.1038/nri3158 · Cited by 1,176
Self-citationon behalf of the EuroFlow Consortium (EU-FP6, L.-C.-2.-0., van Dongen, J. J. M., Lhermitte, L., Böttcher, S., Almeida, J., van der Velden, V. H. J., Flores-Montero, J., Rawstron, A., Asnafi, V, Lécrevisse, Q., et al. (2012) · Leukemia · doi:10.1038/leu.2012.120 · Cited by 934
EuroFlow standardization of flow cytometer instrument settings and immunophenotyping protocols
on behalf of the EuroFlow Consortium (EU-FP6, L.-C.-2.-0., Kalina, T., Flores-Montero, J., van der Velden, V. H. J., Martin-Ayuso, M., Böttcher, S., Ritgen, M., Almeida, J., Lhermitte, L., Asnafi, V, et al. (2012) · Leukemia · doi:10.1038/leu.2012.122 · Cited by 783
Critical assessment of automated flow cytometry data analysis techniques
The FlowCAP Consortium, Aghaeepour, N., The DREAM Consortium, Finak, G., Hoos, H., Mosmann, T. R., Brinkman, R., Gottardo, R., & Scheuermann, R. H. (2013) · Nature Methods · doi:10.1038/nmeth.2365 · Cited by 598
Self-citationParsimony, Exhaustivity and Balanced Detection in Neocortex
Romagnoni, A., Ribot, J., Bennequin, D., & Touboul, J. (2015) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004623 · Cited by 296
Standardization of cytokine flow cytometry assays
Maecker, H. T., Rinfret, A., D'Souza, P., Darden, J., Roig, E., Landry, C., Hayes, P., Birungi, J., Anzala, O., Garcia, M., et al. (2005) · BMC Immunology · doi:10.1186/1471-2172-6-13 · Cited by 241
Self-citationStreitz, M., Miloud, T., Kapinsky, M., Reed, M. R., Magari, R., Geissler, E. K., Hutchinson, J. A., Vogt, K., Schlickeiser, S., Kverneland, A. H., et al. (2013) · Transplantation Research · doi:10.1186/2047-1440-2-17 · Cited by 214
Quality assurance for polychromatic flow cytometry
Perfetto, S. P., Ambrozak, D., Nguyen, R., Chattopadhyay, P., & Roederer, M. (2006) · Nature Protocols · doi:10.1038/nprot.2006.250 · Cited by 199
Finak, G., Frelinger, J., Jiang, W., Newell, E. W., Ramey, J., Davis, M. M., Kalams, S. A., De Rosa, S. C., & Gottardo, R. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003806 · Cited by 197
Self-citationA model for harmonizing flow cytometry in clinical trials
the FOCIS Human Immunophenotyping Consortium, Maecker, H. T., & McCoy, J. P. (2010) · Nature Immunology · doi:10.1038/ni1110-975 · Cited by 155 · cited 1×
“We transformed the proportion, (1): yrij=logit(prij), and model (2):”
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Measurement and Clinical Significance of Biomarkers of Oxidative Stress in Humans
Marrocco, I., Altieri, F., & Peluso, I. (2017) · Oxidative Medicine and Cellular Longevity · doi:10.1155/2017/6501046 · Cited by 855
CytoNorm: A Normalization Algorithm for Cytometry Data
Van Gassen, S., Gaudilliere, B., Angst, M. S., Saeys, Y., & Aghaeepour, N. (2020) · Cytometry Part A · doi:10.1002/cyto.a.23904 · Cited by 234
“While several additional protocol standardization efforts are taking place (7), slight differences in sample handling between multiple batches are unavoidable (8).”
BackgroundSelf-citationTesting for differential abundance in mass cytometry data
Lun, A. T. L., Richard, A. C., & Marioni, J. C. (2017) · Nature Methods · doi:10.1038/nmeth.4295 · Cited by 181
Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy
Hartmann, F. J., Babdor, J., Gherardini, P. F., Amir, E.-A. D., Jones, K., Sahaf, B., Marquez, D. M., Krutzik, P., O’Donnell, E., Sigal, N., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.06.049 · Cited by 124
Self-citationCell type discovery and representation in the era of high-content single cell phenotyping
Bakken, T., Cowell, L., Aevermann, B. D., Novotny, M., Hodge, R., Miller, J. A., Lee, A., Chang, I., McCorrison, J., Pulendran, B., et al. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1977-1 · Cited by 55
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Metadata
- Authors
- Finak, G., Langweiler, M., Jaimes, M., Malek, M., Taghiyar, J., Korin, Y., Raddassi, K., Devine, L., Obermoser, G., Pekalski, M. L., Pontikos, N., Diaz, A., Heck, S., Villanova, F., Terrazzini, N., Kern, F., Qian, Y., Stanton, R., Wang, K., Brandes, A., Ramey, J., Aghaeepour, N., Mosmann, T., Scheuermann, R. H., Reed, E., Palucka, K., Pascual, V., Blomberg, B. B., Nestle, F., Nussenblatt, R. B., Brinkman, R. R., Gottardo, R., Maecker, H., & McCoy, J. P.
- Venue
- Scientific Reports
- Published
- 2016-02-10
- Volume
- 6
- Issue
- 1
- Pages
- 20686-20686
- ISSN
- 2045-2322 (ISSN-L)
- OpenAlex
- W2290269515
- Cited by
- 285
- References
- 23
- FWCI
- 23.73
- Type
- journal article
- Language
- en
- Open access
- gold
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- Finak, G., Langweiler, M., Jaimes, M., Malek, M., Taghiyar, J., Korin, Y., Raddassi, K., Devine, L., Obermoser, G., Pekalski, M. L., Pontikos, N., Diaz, A., Heck, S., Villanova, F., Terrazzini, N., Kern, F., Qian, Y., Stanton, R., Wang, K., . . . McCoy, J. P. (2016). Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium. Scientific Reports. https://doi.org/10.1038/srep20686
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