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bioRxiv · 10.1101/2023.05.15.540875

Robust differential expression testing for single-cell CRISPR screens at low multiplicity of infection

Barry, T.·Mason, K.·Roeder, K.·Katsevich, E.
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Abstract

Single-cell CRISPR screens (perturb-seq) link genetic perturbations to phenotypic changes in individual cells. The most fundamental task in perturb-seq analysis is to test for association between a perturbation and a count outcome, such as gene expression. We conduct the first-ever comprehensive benchmarking study of association testing methods for low multiplicity-of-infection (MOI) perturb-seq data, finding that existing methods produce excess false positives. We conduct an extensive empirical investigation of the data, identifying three core analysis challenges: sparsity, confounding, and model misspecification. Finally, we develop an association testing method -- SCEPTRE low-MOI -- that resolves these analysis challenges and demonstrates improved calibration and power.

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Barry, T., Mason, K., Roeder, K., Katsevich, E.. 2023-05-15. Robust differential expression testing for single-cell CRISPR screens at low multiplicity of infection. https://doi.org/10.1101/2023.05.15.540875

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