Latent modeling of flow cytometry cell populations

Abstract: Flow cytometry is a widespread single-cell measurement technology with a multitude of clinical and research applications. Interpretation of flow cytometry data is hard; the instrumentation is delicate and can not render absolute measurements, hence samples can only be interpreted in relation to each other while at the same time comparisons are confounded by inter-sample variation. Despite this, current automated flow cytometry data analysis methods either treat samples individually or ignore the variation by for example pooling the data. In this article we introduce a Bayesian hierarchical model for studying latent relations between cell populations in flow cytometry samples, thereby systematizing inter-sample variation. The model is applied to a data set containing replicated flow cytometry measurements of samples from healthy individuals, with informative priors capturing expert knowledge. It is shown that the technical variation in the inferred cell population sizes is small in comparison to the intrinsic biological variation. The large size of flow cytometry data, where a single sample can contain measurements on hundreds of thousands of cells, necessitates computationally efficient methods. To address this, we have implemented a parallel Markov Chain Monte Carlo scheme for sampling the posterior distribution.