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CellSIUS provides sensitive and specific detection of rare cell populations from complex single cell RNA-seq data

Neri, Marilisa and Wegmann, Rebekka and Schuierer, Sven and Bilican, Bilada and Hartkopf, Huyen and Mapa, Felipa and Waldt, Annick and Cuttat-Theurillat, Rachel and Salick, Max and Raymond, Joe and Kaykas, Ajamete and Roma, Guglielmo and Gubser Keller, Caroline (2019) CellSIUS provides sensitive and specific detection of rare cell populations from complex single cell RNA-seq data. Genome biology, 20 (142). ISSN 1474-760X; 1474-7596

Abstract

We develop CellSIUS (Cell Subtype Identification from Upregulated gene Sets) to fill a methodology gap for rare cell population identification for scRNA-seq data. CellSIUS outperforms existing algorithms for specificity and selectivity for rare cell types and their transcriptomic signature identification in synthetic and complex biological data. Characterization of a human pluripotent cell differentiation protocol recapitulating deep-layer corticogenesis using CellSIUS reveals unrecognized complexity in human stem cell-derived cellular populations. CellSIUS enables identification of novel rare cell populations and their signature genes providing the means to study those populations in vitro in light of their role in health and disease.

Item Type: Article
Date Deposited: 22 Nov 2019 00:45
Last Modified: 22 Nov 2019 00:45
URI: https://oak.novartis.com/id/eprint/36659

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