Abstract
In the era of consortium-based studies, “omics,” and data sharing, flow cytometry needs to match other technological platforms in terms of standard operating procedures, reduced variability, and reproducibility. While tools such as gene-expression platforms have proven robustness and reproducibility, flow cytometry still relies heavily on scientists for the development of antibody panels as well as detailed experimental procedures. This is expected to remain for several decades, as the limit of markers to be assessed in a single staining does not allow attainment of the “omic” level of other technological platforms. This chapter presents a non-exhaustive series of multi-centric and longitudinal studies and their integration of flow cytometry measures. We also discuss recommendations made by key consortia to minimize variability in flow cytometry experiments. This chapter also aims to raise awareness of factors that may influence flow cytometry data obtained in large studies.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Cossarizza A, Ortolani C, Mussini C, Borghi V, Guaraldi G, Mongiardo N, Bellesia E, Franceschini MG, De Rienzo B, Franceschi C (1995) Massive activation of immune cells with an intact T cell repertoire in acute human immunodeficiency virus syndrome. J Infect Dis 172:105–112
Gatti L, Tenconi PM, Guarneri D, Bertulessi C, Ossola MW, Bosco P, Gianotti GA (1994) Hemostatic parameters and platelet activation by flow-cytometry in normal pregnancy: a longitudinal study. Int J Clin Lab Res 24:217–219
Bradstock K, Matthews J, Benson E, Page F, Bishop J (1994) Prognostic value of immunophenotyping in acute myeloid leukemia. Australian Leukaemia Study Group. Blood 84:1220–1225
Benevolo G, Stacchini A, Spina M, Ferreri AJ, Arras M, Bellio L, Botto B, Bulian P, Cantonetti M, Depaoli L, Di Renzo N, Di Rocco A, Evangelista A, Franceschetti S, Godio L, Mannelli F, Pavone V, Pioltelli P, Vitolo U, Pogliani EM (2012) Final results of a multicenter trial addressing role of CSF flow cytometric analysis in NHL patients at high risk for CNS dissemination. Blood 120:3222–3228
Della Porta MG1, Picone C, Pascutto C, Malcovati L, Tamura H, Handa H, Czader M, Freeman S, Vyas P, Porwit A, Saft L, Westers TM, Alhan C, Cali C, van de Loosdrecht AA, Ogata K (2012) Multicenter validation of a reproducible flow cytometric score for the diagnosis of low-grade myelodysplastic syndromes: results of a European LeukemiaNET study. Haematologica 97:1209–1217
Wikby A, Maxson P, Olsson J, Johansson B, Ferguson FG (1998) Changes in CD8 and CD4 lymphocyte subsets, T cell proliferation responses and non-survival in the very old: the Swedish longitudinal OCTO-immune study. Mech Ageing Dev 102:187–198
Adriaensen W, Pawelec G, Vaes B, Hamprecht K, Derhovanessian E, van Pottelbergh G, Degryse JM, Matheï C (2016) CD4:8 ratio above 5 is associated with all-cause mortality in cmv-seronegative very old women: results from the BELFRAIL study. J Gerontol A Biol Sci Med Sci (in press)
Irving J, Jesson J, Virgo P, Case M, Minto L, Eyre L, Noel N, Johansson U, Macey M, Knotts L, Helliwell M, Davies P, Whitby L, Barnett D, Hancock J, Goulden N, Lawson S; UKALL Flow MRD Group; UK MRD steering Group (2009) Establishment and validation of a standard protocol for the detection of minimal residual disease in B lineage childhood acute lymphoblastic leukemia by flow cytometry in a multi-center setting. Haematologica 94:870–874
McGowan I, Anton PA, Elliott J, Cranston RD, Duffill K, Althouse AD, Hawkins KL, De Rosa SC (2015) Exploring the feasibility of multi-site flow cytometric processing of gut associated lymphoid tissue with centralized data analysis for multi-site clinical trials. PLoS ONE 10:e0126454
Freeman CM, Crudgington S, Stolberg VR, Brown JP, Sonstein J, Alexis NE, Doerschuk CM, Basta PV, Carretta EE, Couper DJ, Hastie AT, Kaner RJ, O’Neal WK, Paine R 3rd, Rennard SI, Shimbo D, Woodruff PG, Zeidler M, Curtis JL (2015) Design of a multi-center immunophenotyping analysis of peripheral blood, sputum and bronchoalveolar lavage fluid in the Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS). J Transl Med 13:19
Giorgi JV, Cheng HL, Margolick JB, Bauer KD, Ferbas J, Waxdal M, Schmid I, Hultin LE, Jackson AL, Park L (1990) Quality control in the flow cytometric measurement of T-lymphocyte subsets: the multicenter AIDS cohort study experience. The Multicenter AIDS Cohort Study Group. Clin Immunol Immunopathol 55:173–186
Stewart JC1, Villasmil ML, Frampton MW (2007) Changes in fluorescence intensity of selected leukocyte surface markers following fixation. Cytometry A 71:379–385
Mair F, Hartmann FJ, Mrdjen D, Tosevski V, Krieg C, Becher B. The end of gating? An introduction to automated analysis of high dimensional cytometry data. Eur J Immunol. 46:34–43
http://www.immudex.com/media/46328/mhc_multimer_proficiency_panel_2015.pdf
Kalina T, Flores-Montero J, van der Velden VH, Martin-Ayuso M, Böttcher S, Ritgen M, Almeida J, Lhermitte L, Asnafi V, Mendonça A, de Tute R, Cullen M, Sedek L, Vidriales MB, Pérez JJ, te Marvelde JG, Mejstrikova E, Hrusak O, Szczepański T, van Dongen JJ, Orfao A (2012) EuroFlow standardization of flow cytometer instrument settings and immunophenotyping protocols. Leukemia 26:1986–2010
Streitz M, Miloud T, Kapinsky M, Reed MR, Magari R, Geissler EK, Hutchinson JA, Vogt K, Schlickeiser S, Kverneland AH, Meisel C, Volk HD, Sawitzki B (2013) Standardization of whole blood immune phenotype monitoring for clinical trials: panels and methods from the ONE study. Transplant Res 2:17
Finak G, Langweiler M, Jaimes M, Malek M, Taghiyar J, Korin Y, Raddassi K, Devine L, Obermoser G, Pekalski ML, 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 RH, Reed E, Palucka K, Pascual V, Blomberg BB, Nestle F, Nussenblatt RB, Brinkman RR, Gottardo R, Maecker H, McCoy JP (2016) Standardizing flow cytometry immunophenotyping analysis from the human immunophenotyping consortium. Sci Rep 6:20686
Bainbridge J, Wilkening CL, Rountree W, Louzao R, Wong J, Perza N, Garcia A, Denny TN (2014) The immunology quality assessment proficiency testing program for CD3+ 4+ and CD3+ 8+ lymphocyte subsets: a ten year review via longitudinal mixed effects modeling. J Immunol Methods 409:82–90
White S, Laske K, Welters MJ, Bidmon N, van der Burg SH, Britten CM, Enzor J, Staats J, Weinhold KJ, Gouttefangeas C, Chan C (2015) managing multi-center flow cytometry data for immune monitoring. Cancer Inf 13:111–122
Schadt EE, Linderman MD, Sorenson J, Lee L, Nolan GP (2016) Computational solutions to large-scale data management and analysis. Nat Rev Genet 11:647–657
Monaco G, Chen H, Poidinger M, Chen J, de Magalhães JP, Larbi A (2016) flowAI: automatic and interactive anomaly discerning tools for flow cytometry data. Bioinformatics 32:2473–2480
Fletez-Brant K, Špidlen J, Brinkman RR, Roederer M, Chattopadhyay PK (2016) flowClean: Automated identification and removal of fluorescence anomalies in flow cytometry data. Cytometry A 89:461–471
Finak G, Jiang W, Pardo J, Asare A, Gottardo R (2012) QUAliFiER: an automated pipeline for quality assessment of gated flow cytometry data. BMC Bioinform 13:252
https://www.bioconductor.org/packages/release/bioc/html/flowQ.html
Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH. Automated analysis of flow cytometry data comes of age. Cytometry A 89:13–15
Kvistborg Pia, Gouttefangeas Cécile, Aghaeepour Nima, Cazaly Angelica, Chattopadhyay Pratip K, Chan Cliburn, Eckl Judith, Finak Greg, Hadrup Sine Reker, Maecker Holden T, Maurer Dominik, Mosmann Tim, Qiu Peng, Scheuermann Richard H, Welters Marij JP, Ferrari Guido, Brinkman Ryan R, Britten Cedrik M (2016) Thinking outside the gate: single-cell assessments in multiple dimensions. Immunity 42:591–592
Guilliams M, Dutertre CA, Scott CL, McGovern N, Sichien D, Chakarov S, Van Gassen S, Chen J, Poidinger M, De Prijck S, Tavernier SJ, Low I, Irac SE, Mattar CN, Sumatoh HR, Low GH, Chung TJ, Chan DK, Tan KK, Hon TL, Fossum E, Bogen B, Choolani M, Chan JK, Larbi A, Luche H, Henri S, Saeys Y, Newell EW, Lambrecht BN, Malissen B, Ginhoux F (2016) Unsupervised high-dimensional analysis aligns dendritic cells across tissues and species. Immunity 45:669–684
Aghaeepour N, Chattopadhyay P, Chikina M, Dhaene T, Van Gassen S, Kursa M, Lambrecht BN, Malek M, McLachlan GJ, Qian Y, Qiu P, Saeys Y, Stanton R, Tong D, Vens C, Walkowiak S, Wang K, Finak G, Gottardo R, Mosmann T, Nolan GP, Scheuermann RH, Brinkman RR (2016) A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes. Cytometry A 89:16–21
Kleinsteuber K, Corleis B, Rashidi N, Nchinda N, Lisanti A, Cho JL, Medoff BD, Kwon D, Walker BD (2016) Standardization and quality control for high-dimensional mass cytometry studies of human samples. Cytometry A 89:903–913
Acknowledgments
Anis Larbi is supported by the Singapore Immunology Network, the Agency for Science Technology and Research (Clinical Immunomonitoring Platform grant #H16/99/b0/0111) and the Joint Council Office Development Program (grant #1434m0011). Anis Larbi is an emeritus Marylou Ingram ISAC Scholar.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Larbi, A. (2017). Flow Cytometry in Multi-center and Longitudinal Studies. In: Robinson, J., Cossarizza, A. (eds) Single Cell Analysis. Series in BioEngineering. Springer, Singapore. https://doi.org/10.1007/978-981-10-4499-1_5
Download citation
DOI: https://doi.org/10.1007/978-981-10-4499-1_5
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-10-4498-4
Online ISBN: 978-981-10-4499-1
eBook Packages: EngineeringEngineering (R0)