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 single-nucleotide 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.

Ramazzotti, D., Angaroni, F., Maspero, D., Ascolani, G., Castiglioni, I., Piazza, R., et al. (2021). Variant calling from scRNA-seq data allows the assessment of cellular identity in patient-derived cell lines [Altro] [10.1101/2021.04.13.439634].

Variant calling from scRNA-seq data allows the assessment of cellular identity in patient-derived cell lines

Ramazzotti, Daniele;Angaroni, Fabrizio;Maspero, Davide;Ascolani, Gianluca;Castiglioni, Isabella;Piazza, Rocco;Antoniotti, Marco;
2021

Abstract

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 single-nucleotide 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.
Altro
No
Scientifica
Cancer research;Singel-cells sequencing
English
Ramazzotti, D., Angaroni, F., Maspero, D., Ascolani, G., Castiglioni, I., Piazza, R., et al. (2021). Variant calling from scRNA-seq data allows the assessment of cellular identity in patient-derived cell lines [Altro] [10.1101/2021.04.13.439634].
Ramazzotti, D; Angaroni, F; Maspero, D; Ascolani, G; Castiglioni, I; Piazza, R; Antoniotti, M; Graudenzi, A
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/10281/311073
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