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Scalable, fast and accurate differential gene expression testing from millions of cells of multiple patients

Santacatterina, G.; Tosato, N.; Milite, S.; Davydzenka, K.; Insaghi, E.; Cozzini, S.; Sanguinetti, G.; Egidi, L.; Caravagna, G.

2025-07-30 bioinformatics
10.1101/2025.07.24.666556 bioRxiv
Show abstract

Since the development of DNA microarrays and later RNA bulk sequencing, testing with statistically independent samples has been the standard method for detecting genes with different transcription patterns. Single-cell assays challenge these assumptions because individual cells are statistically dependent, and all proposed methodologies present mathematical limitations or computational bottlenecks that prevent a seamless integration of data from many cells and patients simultaneously. In this work, we solve this crucial limitation by introducing a Bayesian framework that retrieves the independence structure at the level of individual patients, separating differences across individuals from actual transcriptional differences. Leveraging multi-GPU and variational inference, our approach excels across different experimental designs and, for the first time, scales to analyse over 10 million cells in less than 2 hours. This new framework enables single-cell differential expression analysis that can finally integrate datasets from large clinical cohorts, atlas projects, or drug-response screens with thousands of samples and millions of cells.

Published in Nature Communications (predicted rank #1) · training set

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