B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle
B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle
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DOI：
10.1093/bioinformatics/bty203
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发表时间：
2018-08-15
期刊：
影响因子：
5.8
通讯作者：
Luciani, Fabio
中科院分区：
文献类型：
--
作者：
Rizzetto, Simone;Koppstein, David N. P.;Luciani, Fabio
动机：B细胞受体（BCR）执行适应性免疫系统的基本功能，包括识别病原体衍生的抗原。由于V（D）J重组和体细胞超突变导致的BCR序列的巨大库和适应性变化需要BCR序列的单细胞表征。单细胞RNA测序提供了机会，同时捕获配对的BCR重链和轻链和transcriptomic signature.Results：我们开发了VDJPuzzle，一种新的生物信息学工具，重建生产，全长B细胞受体序列的重链和轻链，并提取体细胞突变的VDJ区域。VDJPuzzle成功地从100%（n = 117）人和96.5%（n = 200）鼠B细胞中重建了BCR。可用性和实施：VDJPuzzle可在https://bitbucket.org/kirbyvisp/vdjpuzzle2.Contact：luciani@ unsw.edu. au上获得补充信息：补充数据可在Bioinformatics在线上获得。
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.Contact: luciani@ unsw.edu.auSupplementary information: Supplementary data are available at Bioinformatics online.