High-speed automatic characterization of rare events in flow cytometric data
Jazyk angličtina Země Spojené státy americké Médium electronic-ecollection
Typ dokumentu časopisecké články
Grantová podpora
P01 HL131477
NHLBI NIH HHS - United States
P30 CA008748
NCI NIH HHS - United States
R35 CA197697
NCI NIH HHS - United States
UL1 TR001863
NCATS NIH HHS - United States
PubMed
32045462
PubMed Central
PMC7012421
DOI
10.1371/journal.pone.0228651
PII: PONE-D-19-22326
Knihovny.cz E-zdroje
- MeSH
- laboratorní automatizace metody MeSH
- pravděpodobnost MeSH
- průtoková cytometrie metody MeSH
- teoretické modely * MeSH
- Publikační typ
- časopisecké články MeSH
A new computational framework for FLow cytometric Analysis of Rare Events (FLARE) has been developed specifically for fast and automatic identification of rare cell populations in very large samples generated by platforms like multi-parametric flow cytometry. Using a hierarchical Bayesian model and information-sharing via parallel computation, FLARE rapidly explores the high-dimensional marker-space to detect highly rare populations that are consistent across multiple samples. Further it can focus within specified regions of interest in marker-space to detect subpopulations with desired precision.
Cancer Science Institute National University of Singapore Singapore Singapore
Center for Life Sciences Harvard Medical School Boston MA United States of America
Department of Cell Biology Yale University School of Medicine New Haven CT United States of America
Department of Computer Science Purdue University West Lafayette IN United States of America
Department of Genetics Yale University School of Medicine New Haven CT United States of America
Department of Statistics Purdue University West Lafayette IN United States of America
Harvard Stem Cell Institute Harvard Medical School Boston MA United States of America
Institute of Molecular Genetics of the ASCR Prague Czech Republic
Population Health Sciences Institute Newcastle University Newcastle upon Tyne United Kingdom
Yale Stem Cell Center Yale University School of Medicine New Haven CT United States of America
Zobrazit více v PubMed
Preffer F, Dombkowski D. Advances in complex multiparameter flow cytometry technology: Applications in stem cell research. Cytometry Part B: Clinical Cytometry. 2009;76B(5):295–314. 10.1002/cyto.b.20480 PubMed DOI PMC
Tanner SD, Bandura DR, Ornatsky O, Baranov VI, Nitz M, Winnik MA. Flow cytometer with mass spectrometer detection for massively multiplexed single-cell biomarker assay. Pure and Applied Chemistry. 2009;80(12):2627–2641. 10.1351/pac200880122627 DOI
Bendall SC, Simonds EF, Qiu P, Amir EaD, Krutzik PO, Finck R, et al. Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum. Science. 2011;332(6030):687–696. 10.1126/science.1198704 PubMed DOI PMC
Pyne S, Hu X, Wang K, Rossin E, Lin TI, Maier LM, et al. Automated high-dimensional flow cytometric data analysis. Proceedings of the National Academy of Sciences. 2009;106(21):8519–8524. 10.1073/pnas.0903028106 PubMed DOI PMC
Qiu P, Simonds EF, Bendall SC, Gibbs KD, Bruggner RV, Linderman MD, et al. Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE. Nature Biotechnology. 2011;29(10):886–891. PubMed PMC
Lee SX, McLachlan GJ, Pyne S. Modeling of inter-sample variation in flow cytometric data with the joint clustering and matching procedure. Cytometry Part A. 2016;89(1):30–43. 10.1002/cyto.a.22789 PubMed DOI
Lugli E, Roederer M, Cossarizza A. Data analysis in flow cytometry: The future just started. Cytometry Part A. 2010;77A(7):705–713. 10.1002/cyto.a.20901 PubMed DOI PMC
Pyne S, Lee SX, Wang K, Irish J, Tamayo P, Nazaire MD, et al. Joint Modeling and Registration of Cell Populations in Cohorts of High-Dimensional Flow Cytometric Data. PLoS ONE. 2014;9(7):e100334 10.1371/journal.pone.0100334 PubMed DOI PMC
Maecker HT, McCoy JP, Nussenblatt R. Standardizing immunophenotyping for the Human Immunology Project. Nature Reviews Immunology. 2012;12(3):191–200. 10.1038/nri3158 PubMed DOI PMC
Cron A, Gouttefangeas C, Frelinger J, Lin L, Singh SK, Britten CM, et al. Hierarchical modeling for rare event detection and cell subset alignment across flow cytometry samples. PLoS Comput Biol. 2013;9(7):e1003130 10.1371/journal.pcbi.1003130 PubMed DOI PMC
Brown D, Kogan S, Lagasse E, Weissman I, Alcalay M, Pelicci PG, et al. A PML–RARα transgene initiates murine acute promyelocytic leukemia. Proceedings of the National Academy of Sciences of the United States of America. 1997;94(6):2551–2556. 10.1073/pnas.94.6.2551 PubMed DOI PMC
Guibal FC, Alberich-Jorda M, Hirai H, Ebralidze A, Levantini E, Di Ruscio A, et al. Identification of a myeloid committed progenitor as the cancer-initiating cell in acute promyelocytic leukemia. Blood. 2009;114(27):5415–5425. 10.1182/blood-2008-10-182071 PubMed DOI PMC
Wojiski S, Guibal FC, Kindler T, Lee BH, Jesneck JL, Fabian A, et al. PML–RARα initiates leukemia by conferring properties of self-renewal to committed promyelocytic progenitors. Leukemia. 2009;23(8):1462–1471. 10.1038/leu.2009.63 PubMed DOI PMC
Lee SX, McLachlan G, Pyne S. In: Pyne S, Rao BLSP, Rao SB, editors. Application of Mixture Models to Large Datasets. New Delhi: Springer India; 2016. p. 57–74. Available from: 10.1007/978-81-322-3628-3_4. DOI
Chan C, Feng F, Ottinger J, Foster D, West M, Kepler TB. Statistical mixture modeling for cell subtype identification in flow cytometry. Cytometry A. 2008;73(8):693–701. 10.1002/cyto.a.20583 PubMed DOI PMC
Ho HJ, Lin TI, Chang HH, Haase SB, Huang S, Pyne S. Parametric modeling of cellular state transitions as measured with flow cytometry. BMC Bioinformatics. 2012;13 Suppl 5:S5 10.1186/1471-2105-13-S5-S5 PubMed DOI PMC
Lin L, Chan C, Hadrup SR, Froesig TM, Wang Q, West M. Hierarchical Bayesian mixture modelling for antigen-specific T-cell subtyping in combinatorially encoded flow cytometry studies. Stat Appl Genet Mol Biol. 2013;12(3):309–331. 10.1515/sagmb-2012-0001 PubMed DOI PMC
Richards AJ, Staats J, Enzor J, McKinnon K, Frelinger J, Denny TN, et al. Setting objective thresholds for rare event detection in flow cytometry. J Immunol Methods. 2014;409:54–61. 10.1016/j.jim.2014.04.002 PubMed DOI PMC
Naim I, Datta S, Rebhahn J, Cavenaugh JS, Mosmann TR, Sharma G. SWIFT-scalable clustering for automated identification of rare cell populations in large, high-dimensional flow cytometry datasets, part 1: algorithm design. Cytometry A. 2014;85(5):408–421. 10.1002/cyto.a.22446 PubMed DOI PMC
Lin L, Frelinger J, Jiang W, Finak G, Seshadri C, Bart PA, et al. Identification and visualization of multidimensional antigen-specific T-cell populations in polychromatic cytometry data. Cytometry A. 2015;87(7):675–682. 10.1002/cyto.a.22623 PubMed DOI PMC
Aghaeepour N, Nikolic R, Hoos HH, Brinkman RR. Rapid cell population identification in flow cytometry data. Cytometry A. 2011;79(1):6–13. 10.1002/cyto.a.21007 PubMed DOI PMC
Ge Y, Sealfon SC. flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding. Bioinformatics. 2012;28(15):2052–2058. 10.1093/bioinformatics/bts300 PubMed DOI PMC
Ye X, Ho JWK. Ultrafast clustering of single-cell flow cytometry data using FlowGrid. BMC Systems Biology. 2019;13(2):35 10.1186/s12918-019-0690-2 PubMed DOI PMC