Single-cell classification using learned cell phenotypes

Single-cell methods such as flow cytometry, Mass cytometry and single-cell mRNA sequencing collect high-dimensional data on thousands to millions of individual cells. An important aim during the analysis of such data is to classify cells into known categories and cell types. One commonly used approach towards this is clustering of cells with similar features followed by manual annotation of clusters in relation to known biology. A second approach, commonly used for cytometry data relies on manual sorting or “gating” of cells, often based on pairwise combinations of measurements used in a stepwise and very tedious process of cell annotation. Both of these approaches require manual inspection and annotation of every new dataset generated, a process that is not only time consuming but also subjective and surely influential for the conclusions drawn. The manual annotation is also difficult to reproduce by other researchers with a different perception of features that signify their cells of interest. Here we propose an alternative strategy based on machine learning of known phenotypes from manually curated, high-dimensional data and thereby enabling rapid classification of subsequent datasets in a more reproducible manner. This simple approach increases both throughput, reproducibility and simplicity of cell classification in single-cell biology.