Polychromatic flow cytometry: a rapid method for the reduction and analysis of complex multiparameter data

Cytometry A. 2006 Dec 1;69(12):1162-73. doi: 10.1002/cyto.a.20342.


Background: Recent advances in flow cytometry have resulted in the development of reliable techniques for performing polychromatic (5-17 color) flow cytometry analysis. However, the data reduction and analysis involved in the resolution of hundreds of possible cellular subphenotypes identified, using a single polychromatic flow cytometry staining panel, presents a major obstacle to the successful application of this technology.

Methods: To generate two distinct collections of T cell populations with differentially expressed surface markers, cryopreserved lymph node cells from 5 melanoma patients vaccinated with the modified gp100(209-2M) melanoma peptide were stimulated with cognate peptide and cultured in either IL-21 + low-dose IL-2 or IL-15 + low-dose IL-2. In vitro stimulated (IVS) cells were interrogated using 8-color flow cytometry. Data were analyzed using Winlist Hyperlog and FCOM software, and 32 T cell subsets were resolved for each culture condition. Hierarchical clustering analysis was applied to the relative percentages of each subphenotype for both IVS conditions to determine if unique cell surface marker expression signatures were produced for each IVS culture.

Results: Sequential data analysis using Hyperlog and FCOM demonstrated that lymphocytes cultured in IL-21 + IL-2 had a distinctively different set of subphenotype signatures compared to cells grown in IL-15 + IL-2 for all 5 patients. Importantly, subsequent cluster analysis of all 32 subphenotype frequencies in each IVS test condition for all 5 patients reproducibly demonstrated that cellular subphenotypes produced after IL-21 + IL-2 IVS partitioned separately from subphenotypes produced by IL-15 + IL-2 IVS.

Conclusions: The integrated sequential use of Hyperlog and FCOM software with cluster analysis algorithms for the reduction and analysis of polychromatic flow cytometry data produces an effective, rapid technique for the assessment of complex patterns of subphenotype expression between and within multiple test samples. This approach to data analysis may enhance the use of polychromatic flow cytometry for both research and clinical applications.

Publication types

  • Evaluation Study
  • Randomized Controlled Trial
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Cells, Cultured
  • Cluster Analysis
  • Flow Cytometry / methods*
  • Humans
  • Interleukin-2 / pharmacology*
  • Interleukin-5 / pharmacology*
  • Interleukins / pharmacology*
  • Lymph Nodes / drug effects
  • T-Lymphocytes / drug effects*


  • Interleukin-2
  • Interleukin-5
  • Interleukins
  • interleukin-21