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

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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.).

Author information

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.

Competing interests

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

Correspondence to Michael J. T. Stubbington.

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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Fig. 1: Example graphical output from BraCeR.