RT Journal Article
SR Electronic
T1 Variant calling from scRNA-seq data allows the assessment of cellular identity in patient-derived cell lines
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.04.13.439634
DO 10.1101/2021.04.13.439634
A1 Daniele Ramazzotti
A1 Fabrizio Angaroni
A1 Davide Maspero
A1 Gianluca Ascolani
A1 Isabella Castiglioni
A1 Rocco Piazza
A1 Marco Antoniotti
A1 Alex Graudenzi
YR 2021
UL http://biorxiv.org/content/early/2021/04/14/2021.04.13.439634.abstract
AB Matters Arising from: Sharma, A., Cao, E.Y., Kumar, V. et al. Longitudinal single-cell RNA sequencing of patient-derived primary cells reveals drug-induced infidelity in stem cell hierarchy. Nat Commun 9, 4931 (2018). https://doi.org/10.1038/s41467-018-07261-3.In Sharma, A. et al. Nat Commun 9, 4931 (2018) the authors employ longitudinal single-cell transcriptomic data from patient-derived primary and metastatic oral squamous cell carcinomas cell lines, to investigate possible divergent modes of chemo-resistance in tumor cell subpopulations. We integrated the analyses presented in the manuscript, by performing variant calling from scRNA-seq data via GATK Best Practices. As a main result, we show that an extremely high number of singlenucleotide variants representative of the identity of a specific patient is unexpectedly found in the scRNA-seq data of the cell line derived from a second patient, and vice versa. This finding likely suggests the existence of a sample swap, thus jeopardizing some of the translational conclusions of the article. Our results prove the efficacy of a joint analysis of the genotypic and transcriptomic identity of single-cells.Competing Interest StatementThe authors have declared no competing interest.