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UMI or not UMI, that is the question for scRNA-seq zero-inflation

Nature Biotechnology volume 39, pages 158–159 (2021)Cite this article

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Matters Arising to this article was published on 01 February 2021

The Original Article was published on 14 January 2020

arising from V. Svensson Nature Biotechnology https://doi.org/10.1038/s41587-019-0379-5 (2020)

In your February 2020 issue, Svensson1 addressed the problem of zero-inflation in single-cell RNA-sequencing (scRNA-seq) data—that is, the observation that more genes in more cells than expected appear to have zero expression. Using examples, the Correspondence demonstrates that droplet-based methods that make use of unique molecular identifier (UMI)2,3 counts to quantify gene expression are adequately modeled with negative binomial distributions without zero-inflation. We agree with this, and we also share the concern that there is confusion about the validity of zero-inflation and the necessity of computational methods to eliminate it.

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Fig. 1: A comparison of the effect of UMI use and the sequencing platform on zero-inflation.

References

  1. Svensson, V. Droplet scRNA-seq is not zero-inflated Nat. Biotechnol. 38, 147–150 (2020).

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Acknowledgements

We thank Deutsche Forschungsgemeinschaft for funding (grants KU1315/14-1 and HO1582/12-1).

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Authors and Affiliations

  1. Bioinformatics and Computational Biophysics, Faculty of Biology and Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany

    Yingying Cao, Simo Kitanovski & Daniel Hoffmann

  2. Institute of Cell Biology (Cancer Research), University Hospital Essen, Essen, Germany

    Ralf Küppers

Authors
  1. Yingying Cao
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  2. Simo Kitanovski
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  3. Ralf Küppers
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  4. Daniel Hoffmann
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Contributions

Y.C. analyzed data and wrote the first draft, S.K. and R.K. reviewed work and revised the text, D.H. supervised work and wrote the final text.

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Correspondence to Daniel Hoffmann.

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The authors declare no competing interests.

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Peer review information Nature Biotechnology thanks the anonymous reviewers for their contribution to the peer review of this work.

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Cao, Y., Kitanovski, S., Küppers, R. et al. UMI or not UMI, that is the question for scRNA-seq zero-inflation. Nat Biotechnol 39, 158–159 (2021). https://doi.org/10.1038/s41587-020-00810-6

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