Cytofast: A workflow for visual and quantitative analysis of flow and mass cytometry data to discover immune signatures and correlations

Beyrend, Guillaume; Stam, Koen; Höllt, T.; Ossendorp, Ferry; Arens, Ramon

doi:10.1016/j.csbj.2018.10.004

Cytofast

Title

Cytofast: A workflow for visual and quantitative analysis of flow and mass cytometry data to discover immune signatures and correlations

Author

Beyrend, Guillaume (Leiden University Medical Center)
Stam, Koen (Leiden University Medical Center)
Höllt, T. (TU Delft Computer Graphics and Visualisation)
Ossendorp, Ferry (Leiden University Medical Center)
Arens, Ramon (Leiden University Medical Center)

Date

2018

Abstract

Multi-parametric flow and mass cytometry allows exceptional high-resolution exploration of the cellular composition of the immune system. A large panel of computational tools have been developed to analyze the high-dimensional landscape of the data generated. Analysis frameworks such as FlowSOM or Cytosplore incorporate clustering and dimensionality reduction techniques and include algorithms allowing visualization of multi-parametric cytometric analysis. To additionally provide means to quantify specific cell clusters and correlations between samples, we developed an R-package, called cytofast, for further downstream analysis. Specifically, cytofast enables the visualization and quantification of cell clusters for an efficient discovery of cell populations associated with diseases or physiology. We used cytofast on mass and flow cytometry datasets based on the modulation of the immune system upon immunotherapy. With cytofast, we rapidly generated visual representations of group-related immune cell clusters and showed correlations with the immune system composition. We discovered macrophage subsets that significantly decrease upon cancer immunotherapy and distinct prime-boost effects of prophylactic vaccines on the myeloid compartment. Cytofast is a time-efficient tool for comprehensive cytometric analysis to reveal immune signatures and correlations. Cytofast is available at Bioconductor.

Subject

Flow and mass cytometry analysis
High-dimensional analysis
R-based package
Single-cell analysis
Visualization tool

To reference this document use:

http://resolver.tudelft.nl/uuid:8f3ab290-6ec8-4fcf-898d-7e91f86e00bd

DOI

https://doi.org/10.1016/j.csbj.2018.10.004

ISSN

2001-0370

Source

Computational and Structural Biotechnology Journal, 16, 435-442

Part of collection

Institutional Repository