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BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq

Nature Methods volume 15, pages 563–565 (2018)Cite this article

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Fig. 1: Example graphical output from BraCeR.

References

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Acknowledgements

We thank K.E.A. Lundin at Oslo University Hospital for providing clinical material; E.S. Fasouli, A. Jinat, and L.M. Eggesbø for assistance with experiments; and S. Kleinstein for helpful discussions. This work was funded by the University of Oslo world-leading research program on human immunology (WL-IMMUNOLOGY; to L.M.S.), the South-Eastern Norway Regional Health Authority (projects 2014045 and 2016113; to L.M.S.), Stiftelsen KG Jebsen (SKGHMED-017 to L.M.S.), the Wellcome Trust (grant 206194 to M.J.T.S., S.A.T., G.E., L.M., and K.P.), and ERC (grant ThDEFINE (646794) to S.A.T.).

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Author notes

  1. Michael J. T. Stubbington

    Present address: 10x Genomics, Leiden, the Netherlands

Authors and Affiliations

  1. Centre for Immune Regulation, University of Oslo and Oslo University Hospital, Oslo, Norway

    Ida Lindeman, Omri Snir, Shuo-Wang Qiao & Ludvig M. Sollid

  2. Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway

    Ida Lindeman, Omri Snir, Shuo-Wang Qiao & Ludvig M. Sollid

  3. Wellcome Sanger Institute, Hinxton, UK

    Ida Lindeman, Guy Emerton, Lira Mamanova, Krzysztof Polanski, Sarah A. Teichmann & Michael J. T. Stubbington

  4. KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway

    Shuo-Wang Qiao & Ludvig M. Sollid

  5. Theory of Condensed Matter, Cavendish Laboratory, Cambridge, UK

    Sarah A. Teichmann

Authors
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Contributions

I.L., M.J.T.S., G.E., and K.P. developed the software. I.L., L.M., O.S., and S.-W.Q. performed scRNA-seq. I.L. analyzed the data. M.J.T.S., L.M.S., and S.A.T. supervised the project. I.L. and M.J.T.S. wrote the manuscript.

Corresponding author

Correspondence to Michael J. T. Stubbington.

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Competing interests

M.J.T.S. has been employed by 10x Genomics since April 2018; this employment had no bearing on this work.

Supplementary Information

Supplementary text and figures

Supplementary Methods, Supplementary Notes 1–8, and Supplementary Tables 1, 7, and 9

Reporting Summary

Supplementary Table 2

Detailed comparison of the most highly expressed heavy and light chain sequences from batch 1 of the mouse dataset (84 cells) reconstructed by BraCeR and BASIC

Supplementary Table 3

Detailed comparison of the most highly expressed heavy and light chain sequences from the human PW2 and PW3 datasets (174 cells) reconstructed by BraCeR and BASIC

Supplementary Table 4

Detailed list of all BCR recombinants reconstructed by BraCeR for the mouse dataset (84 cells)

Supplementary Table 5

Detailed list of all BCR recombinants reconstructed by BraCeR for the human datasets (174 cells)

Supplementary Table 6

Comparison of the IMGT/V-QUEST allele calls of the most highly expressed heavy and light chain sequences from the PW2 human dataset (84 cells) reconstructed by BraCeR and BASIC to allele calls of BCR-targeted Sanger sequencing data

Supplementary Table 8

Comparison of the BraCeR-reconstructed sequences to the targeted BCR-sequencing results for the multiple-chain reconstruction validation experiment

Supplementary Table 10

Primers used for PCR-based verification of BraCeR

Supplementary Software

BraCeR source code and accessory files

Supplementary Data

Source Data for Figure SN4.2 (Supplementary Note 4)

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Lindeman, I., Emerton, G., Mamanova, L. et al. BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq. Nat Methods 15, 563–565 (2018). https://doi.org/10.1038/s41592-018-0082-3

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