T. Abdelaal*1,3, A. Mahfouz1,3, T. Höllt2,3, V.V. Unen4, F. Koning4, B.P.F. Lelieveldt1,3, M.J.T. Reinders1,3
1Delft Bioinformatics Lab, 2Computer Graphics and Visualization, Delft University of Technology, The Netherlands, 3Computational Biology Center, 4Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, The Netherlands
Introduction: High-dimensional mass cytometry (CyTOF) permits the simultaneous measurement of many cellular markers, providing a system-wide view of immune phenotypes at the single-cell level1. Yet, the maximum number of markers that can be measure simultaneously is limited to ~50 due to several technical challenges. We propose a new method to integrate CyTOF data from several marker panels that include an overlapping set of markers, allowing for a deeper interrogation of the cellular composition of the immune system.
Materials & Methods: Given that the maximum number of markers on a CyTOF panel is N. The goal of our study is to expand the number of markers per cell by integrating measurements from two panels which share m markers. The remaining slots can be used to measure (N-m) markers that are unique to each panel. By combining the data, we can extend the number of markers per cell to 2N-m. We created a simulated dataset by selecting the CD8+ T cells lineage (~460k cells, 32 markers) from a recent study1. We split the dataset into two halves (A and B), with cells in A represented by m+k1 and cells in B represented by m+k2 markers. The shared markers m were identified using three methods: PCA, Auto Encoder neural network, and HSNE2. The remaining N-m markers are split into the non-overlapping sets k1 and k2. We used KNN (K = 20) to impute the values of the k2 markers in A (not measured) using the k2 measurements from B, and vice versa.
Results & Discussion: To evaluate our method, we calculated the Euclidian distance between the imputed and measured marker values of each cell and compared them to all the pairwise distances in the lineage (mean±std = 8.6±0.9). The obtained distances for the different values of m are: 2.3±0.8 (m=4), 2.0±0.7 (m=8), 1.6±0.7 (m=12) and 1.6±0.7 (m=15). These preliminary results illustrate the feasibility of using a smaller subset of markers to represent the CD8+ T cells lineage, providing a basis for an approach to extend the number of markers by combining data from multiple panels.
V.V. Unen et al., Immunity (44): 1227-1239, 2016.
N. Pezzotti et al., EuroVis (35): 3, 2016. Funding
Research is part of the ISPIC project, funded by the Marie Curie in the HORIZON 2020 program of the European Commission (H2020-MSCA-ITN-2015)
Credits: None available.
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