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Bioinform

CyTOFmerge: integrating mass cytometry data across multiple panels

Tamim Abdelaal, Thomas Höllt, Vincent van Unen, Boudewijn P. F. Lelieveldt, Frits Koning, Marcel Reinders, and Ahmed Mahfouz

CyTOFmerge pipeline: Split the sample, stain each partial sample with a different marker panel and apply CyTOF to obtain the panels’ measurements. Both panels A and B share a set of markers m (green). L1 (red) are unique markers of panel A, and L2 (blue) are unique markers of panel B. Both panel measurements are combined to obtain an extended markers measurements per cell, which is input to downstream computational analysis as, for example, clustering in a t-SNE mapped domain shown here.

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High-dimensional mass cytometry (CyTOF) allows the simultaneous measurement of multiple cellular markers at single cell level, providing a comprehensive view of cell compositions. However, the power of CyTOF to explore the full heterogeneity of a biological sample at the single cell level is currently limited by the number of markers measured simultaneously on a single panel. To extend the number of markers per cell, we propose an in silico method to integrate CyTOF datasets measured using multiple panels that share a set of markers. Additionally, we present an approach to select the most informative markers from an existing CyTOF dataset to be used as a shared marker set between panels. We demonstrate the feasibility of our methods by evaluating the quality of clustering and neighborhood preservation of the integrated dataset, on two public CyTOF datasets. We illustrate that by computationally extending the number of markers we can further untangle the heterogeneity of mass cytometry data, including rare cell population detection.

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Tamim Abdelaal, Thomas Höllt, Vincent van Unen, Boudewijn P. F. Lelieveldt, Frits Koning, Marcel Reinders, and Ahmed Mahfouz, CyTOFmerge: integrating mass cytometry data across multiple panels, Bioinform, 35, pp. 4063–4071, 2019.

BibTex 

@article{bib:abdelaal:2019,
    author       = { Abdelaal, Tamim and Höllt, Thomas and van Unen, Vincent and Lelieveldt, Boudewijn P. F. and Koning, Frits and Reinders, Marcel and Mahfouz, Ahmed },    
    title        = { CyTOFmerge: integrating mass cytometry data across multiple panels },
    journal      = { Bioinform },
    volume       = { 35 },
    year         = { 2019 },
    pages        = { 4063--4071 },
    doi          = { 10.1093/bioinformatics/btz180 },
    dblp         = { journals/bioinformatics/AbdelaalHULKRM19 },
    url          = { https://publications.graphics.tudelft.nl/papers/105 },
}