The increasing use of mass cytometry for analyzing clinical samples offers the possibility to perform comparative analyses across public datasets. However, challenges in batch normalization and data integration limit the comparison of datasets not intended to be analyzed together. Here, we present a data integration strategy, CytofIn, using generalized anchors to integrate mass cytometry datasets from the public domain. We show that low-variance controls, such as healthy samples and stable channels, are inherently homogeneous, robust against stimulation, and can serve as generalized anchors for batch correction. Single-cell quantification comparing mass cytometry data from 989 leukemia files pre- and post normalization with CytofIn demonstrates effective batch correction while recapitulating the gold-standard bead normalization. CytofIn integration of public cancer datasets enabled the comparison of immune features across histologies and treatments. We demonstrate the ability to integrate public datasets without necessitating identical control samples or bead standards for fast and robust analysis using CytofIn.

Lo, Y., Keyes, T., Jager, A., Sarno, J., Domizi, P., Majeti, R., et al. (2022). CytofIn enables integrated analysis of public mass cytometry datasets using generalized anchors. NATURE COMMUNICATIONS, 13(1) [10.1038/s41467-022-28484-5].

CytofIn enables integrated analysis of public mass cytometry datasets using generalized anchors

Sarno J.;
2022

Abstract

The increasing use of mass cytometry for analyzing clinical samples offers the possibility to perform comparative analyses across public datasets. However, challenges in batch normalization and data integration limit the comparison of datasets not intended to be analyzed together. Here, we present a data integration strategy, CytofIn, using generalized anchors to integrate mass cytometry datasets from the public domain. We show that low-variance controls, such as healthy samples and stable channels, are inherently homogeneous, robust against stimulation, and can serve as generalized anchors for batch correction. Single-cell quantification comparing mass cytometry data from 989 leukemia files pre- and post normalization with CytofIn demonstrates effective batch correction while recapitulating the gold-standard bead normalization. CytofIn integration of public cancer datasets enabled the comparison of immune features across histologies and treatments. We demonstrate the ability to integrate public datasets without necessitating identical control samples or bead standards for fast and robust analysis using CytofIn.
Articolo in rivista - Articolo scientifico
Algorithms; Computational Biology; Datasets as Topic; Flow Cytometry; Humans; Immune Checkpoint Inhibitors; Lymphocytes, Tumor-Infiltrating; Melanoma; Neoplasms; Single-Cell Analysis; Skin Neoplasms
English
17-feb-2022
2022
13
1
934
open
Lo, Y., Keyes, T., Jager, A., Sarno, J., Domizi, P., Majeti, R., et al. (2022). CytofIn enables integrated analysis of public mass cytometry datasets using generalized anchors. NATURE COMMUNICATIONS, 13(1) [10.1038/s41467-022-28484-5].
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/524282
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