B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle

Rizzetto, S.; Koppstein, D. N.; Samir, J.; Singh, M.; Reed, J. H.; Cai, C. H.; Lloyd, A. R.; Eltahla, A. A.; Goodnow, C. C.; Luciani, F.

doi:10.1101/181156

bioRxiv · 10.1101/181156

B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle

Rizzetto, S.·Koppstein, D. N.·Samir, J.·Singh, M.·Reed, J. H.·Cai, C. H.·Lloyd, A. R.·Eltahla, A. A.·Goodnow, C. C.·Luciani, F.

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Abstract

The B-cell receptor (BCR) performs essential functions for the adaptive immune system including recognition of pathogen-derived antigens. Cell-to-cell variability of BCR sequences due to V(D)J recombination and somatic hypermutation (SHM) necessitates single-cell characterization of BCR sequences. Single-cell RNA sequencing (scRNA-seq) presents the opportunity for simultaneous capture of the BCR sequence and transcriptomic signature for a detailed understanding of the dynamics of an immune response.\n\nWe developed VDJPuzzle 2.0, a bioinformatic tool that reconstructs productive, full-length B-cell receptor sequences of both heavy and light chains. VDJPuzzle successfully reconstructs BCRs from 98.3% (n=117) of human and 96.5% (n=200) from murine B cells. 92.0% of clonotypes and 90.3% of mutations were concordant with single-cell Sanger sequencing of the immunoglobulin chains. VDJPuzzle is available at https://bitbucket.org/kirbyvisp/vdjpuzzle2

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Rizzetto, S., Koppstein, D. N., Samir, J., Singh, M., Reed, J. H., Cai, C. H., Lloyd, A. R., Eltahla, A. A., Goodnow, C. C., Luciani, F.. 2017-08-26. B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle. https://doi.org/10.1101/181156

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