B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle
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 char...
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Veröffentlicht in: | Bioinformatics 2018-08, Vol.34 (16), p.2846-2847 |
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Sprache: | eng |
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Zusammenfassung: | 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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ISSN: | 1367-4803 1460-2059 1367-4811 |
DOI: | 10.1093/bioinformatics/bty203 |