SPICE: Exploration and Analysis of Post-Cytometric Complex Multivariate Datasets

By Mario Roederer, Joshua Nozzi, Martha C. Nason. Cytometry Part A, 2011

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Polychromatic flow cytometry results in complex, multivariate datasets. To date, tools for the aggregate analysis of these datasets across multiple specimens grouped by different categorical variables, such as demographic information, have not been optimized. Often, the exploration of such datasets is accomplished by visualization of patterns with pie charts or bar charts, without easy access to statistical comparisons of measurements that comprise multiple components. Here we report on algorithms and a graphical interface we developed for these purposes. In particular, we discuss thresholding necessary for accurate representation of data in pie charts, the implications for display and comparison of normalized versus unnormalized data, and the effects of averaging when samples with significant background noise are present. Finally, we define a statistic for the nonparametric comparison of complex distributions to test for difference between groups of samples based on multi‐component measurements. While originally developed to support the analysis of T cell functional profiles, these techniques are amenable to a broad range of datatypes. Published 2011 Wiley‐Liss, Inc.

Subfields: Biophysics, Immunology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/00f8db50325e1b2b7f2ffb8f1282e33bf6ec585c

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Citations in the corpus

Redistribution, hyperproliferation, activation of natural killer cells and CD8 T cells, and cytokine production during first-in-human clinical trial of recombinant human interleukin-15 in patients with cancer. (2015, methodology): “Flow-Cytometry Analysis Polychromatic flow-cytometry analysis was performed, as described previously, on heparinized blood preinfusion and at various times after the first infusion, with analysis of multiple leukocyte populations including naïve, central memory, and effector memory CD4 and CD8 T cel”
mRNA Vaccines Induce Durable Immune Memory to SARS-CoV-2 and Variants of Concern (2021, methodology): “For Boolean analysis of variant cross-binding, data were imported into SPICE 6 (NIH Vaccine Research Center (55)).”
Follicular helper T cells serve as the major CD4 T cell compartment for HIV-1 infection, replication, and production (2013, methodology): “21; developed by M. Roederer, National Institutes of Health; Roederer et al., 2011).”
Identification and visualization of multidimensional antigen-specific T-cell populations in polychromatic cytometry data (2015, methodology): “…poorly as the numbers of markers increases, and are a poor representation of polyfunctional populations, while representation of polyfunctional profiles via pie charts can be misleading, and depending on the cell population used to normalize the data, significant differences can be obscured (19).”
Exhaustion of tumor-specific CD8⁺ T cells in metastases from melanoma patients. (2011, methodology): “Roederer M, Nozzi JL, Nason MC. SPICE: Exploration and analysis of post-cytometric complex multivariate datasets.”