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

The B-cell receptor (BCR) performs essential functions for the adaptive immune system including recognition of pathogen-derived antigens. The vast repertoire and adaptive variation 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 paired BCR heavy and light chains and the transcriptomic signature.

Researchers from the UNSW, Sydney developed VDJPuzzle, a novel bioinformatic tool that reconstructs productive, full-length B-cell receptor sequences of both heavy and light chains and extract somatic mutations on the VDJ region. VDJPuzzle successfully reconstructed BCRs from 100% (n = 117) human and 96.5% (n = 200) murine B cells. The reconstructed BCRs were successfully validated with single-cell Sanger sequencing.

VDJPuzzle workflow

rna-seq

Availability: VDJPuzzle is available at https://bitbucket.org/kirbyvisp/vdjpuzzle2

Rizzetto S, Koppstein DNP, Samir J, Singh M, Reed JH, Cai CH, Lloyd AR, Eltahla AA, Goodnow CC, Luciani F. (2018) B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle. Bioinformatics [Epub ahead of print]. [abstract]

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