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Blampey Q, Bercovici N, Dutertre CA, Pic I, Ribeiro JM, André F, Cournède PH. A biology-driven deep generative model for cell-type annotation in cytometry. Brief Bioinform 2023; 24:bbad260. [PMID: 37497716 DOI: 10.1093/bib/bbad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/28/2023] Open
Abstract
Cytometry enables precise single-cell phenotyping within heterogeneous populations. These cell types are traditionally annotated via manual gating, but this method lacks reproducibility and sensitivity to batch effect. Also, the most recent cytometers-spectral flow or mass cytometers-create rich and high-dimensional data whose analysis via manual gating becomes challenging and time-consuming. To tackle these limitations, we introduce Scyan https://github.com/MICS-Lab/scyan, a Single-cell Cytometry Annotation Network that automatically annotates cell types using only prior expert knowledge about the cytometry panel. For this, it uses a normalizing flow-a type of deep generative model-that maps protein expressions into a biologically relevant latent space. We demonstrate that Scyan significantly outperforms the related state-of-the-art models on multiple public datasets while being faster and interpretable. In addition, Scyan overcomes several complementary tasks, such as batch-effect correction, debarcoding and population discovery. Overall, this model accelerates and eases cell population characterization, quantification and discovery in cytometry.
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Affiliation(s)
- Quentin Blampey
- Université Paris-Saclay, CentraleSupélec, Laboratory of Mathematics and Computer Science (MICS), 3 rue Joliot Curie, 91190,Gif-sur-Yvette, France
| | - Nadège Bercovici
- Université Paris-Saclay, Gustave Roussy, Inserm U981, 114 Rue Edouard Vaillant, 94805, Villejuif, France
- Université Paris Cité, Institut Cochin, CNRS, Inserm, 22 Rue Méchain, 75014, Paris, France
| | - Charles-Antoine Dutertre
- Université Paris-Saclay, Gustave Roussy, Inserm U1015, 114 Rue Edouard Vaillant, 94805, Villejuif, France
| | - Isabelle Pic
- Université Paris-Saclay, Gustave Roussy, Inserm U981, 114 Rue Edouard Vaillant, 94805, Villejuif, France
| | - Joana Mourato Ribeiro
- Université Paris-Saclay, Gustave Roussy, Inserm U981, 114 Rue Edouard Vaillant, 94805, Villejuif, France
- Gustave Roussy, Département de Médecine Oncologique, 114 Rue Edouard Vaillant, 94805, Villejuif, France
| | - Fabrice André
- Université Paris-Saclay, Gustave Roussy, Inserm U981, 114 Rue Edouard Vaillant, 94805, Villejuif, France
- Gustave Roussy, Département de Médecine Oncologique, 114 Rue Edouard Vaillant, 94805, Villejuif, France
| | - Paul-Henry Cournède
- Université Paris-Saclay, CentraleSupélec, Laboratory of Mathematics and Computer Science (MICS), 3 rue Joliot Curie, 91190,Gif-sur-Yvette, France
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