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Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

Nature Biotechnology volume 36, pages 421427 (2018) | Download Citation


Large-scale single-cell RNA sequencing (scRNA-seq) data sets that are produced in different laboratories and at different times contain batch effects that may compromise the integration and interpretation of the data. Existing scRNA-seq analysis methods incorrectly assume that the composition of cell populations is either known or identical across batches. We present a strategy for batch correction based on the detection of mutual nearest neighbors (MNNs) in the high-dimensional expression space. Our approach does not rely on predefined or equal population compositions across batches; instead, it requires only that a subset of the population be shared between batches. We demonstrate the superiority of our approach compared with existing methods by using both simulated and real scRNA-seq data sets. Using multiple droplet-based scRNA-seq data sets, we demonstrate that our MNN batch-effect-correction method can be scaled to large numbers of cells.

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We are grateful to F.K. Hamey, J.P. Munro, J. Griffiths and M. Büttner for helpful discussions. L.H. was supported by Wellcome Trust Grant 108437/Z/15 to J.C.M. A.T.L.L. was supported by core funding from CRUK (award number 17197 to J.C.M.). M.D.M. was supported by Wellcome Trust Grant 105045/Z/14/Z to J.C.M. J.C.M. was supported by core funding from EMBL and from CRUK (award number 17197).

Author information


  1. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.

    • Laleh Haghverdi
    •  & John C Marioni
  2. Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany.

    • Laleh Haghverdi
  3. Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.

    • Aaron T L Lun
    •  & John C Marioni
  4. Wellcome Trust Sanger Institute, Cambridge, UK.

    • Michael D Morgan
    •  & John C Marioni


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L.H. developed the method and the computational tools, performed the analysis and wrote the paper. A.T.L.L. developed the method and the computational tools and wrote the paper. M.D.M. developed the method, performed the analysis and wrote the paper. J.C.M. developed the method, wrote the paper and supervised the study.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to John C Marioni.

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