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. 2018 Aug 15;34(16):2846-2847.
doi: 10.1093/bioinformatics/bty203.

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

Simone Rizzetto  1   2 , David N P Koppstein  1   2 , Jerome Samir  1   2 , Mandeep Singh  3 , Joanne H Reed  3 , Curtis H Cai  1   2 , Andrew R Lloyd  2 , Auda A Eltahla  1   2 , Christopher C Goodnow  3 , Fabio Luciani  1   2   3
Affiliations

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

Simone Rizzetto et al. Bioinformatics. .

Abstract

Motivation: 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 necessitates single-cell characterization of BCR sequences. Single-cell RNA sequencing presents the opportunity for simultaneous capture of paired BCR heavy and light chains and the transcriptomic signature.

Results: We 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.

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

Supplementary information: Supplementary data are available at Bioinformatics online.

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