B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle
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 (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. 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: VDJPuzzle is available at https://bitbucket.org/kirbyvisp/vdjpuzzle2. Contact: email@example.com. Supplementary Information: Supplementary data are available at Bioinformatics online.
|ISBN||1367-4811 (Electronic) 1367-4803 (Linking)|
|Authors||Rizzetto, S.; Koppstein, D. N. P.; Samir, J.; Singh, M.; Reed, J. H.; Cai, C. H.; Lloyd, A. R.; Eltahla, A. A.; Goodnow, C. C.; Luciani, F.|
|Responsible Garvan Author||Prof Christopher Goodnow|
|URL link to publisher's version||https://www.ncbi.nlm.nih.gov/pubmed/29659703|