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

被引：72

作者：

Rizzetto, Simone ^{[1
,2
]}

Koppstein, David N. P. ^{[1
,2
]}

Samir, Jerome ^{[1
,2
]}

Singh, Mandeep ^{[3
]}

Reed, Joanne H. ^{[3
]}

Cai, Curtis H. ^{[1
,2
]}

Lloyd, Andrew R. ^{[2
]}

Eltahla, Auda A. ^{[1
,2
]}

Goodnow, Christopher C. ^{[3
]}

Luciani, Fabio ^{[1
,2
,3
]}

机构：

[1] UNSW, Kirby Inst Infect & Immun, Sydney, NSW, Australia

[2] UNSW, Sch Med Sci, Sydney, NSW, Australia

[3] Garvan Inst Med Res, Immunogen, Sydney, NSW, Australia

来源：

BIOINFORMATICS | 2018年 / 34卷 / 16期

基金：

英国医学研究理事会; 澳大利亚国家健康与医学研究理事会;

关键词：

D O I：

10.1093/bioinformatics/bty203

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.au Supplementary information: Supplementary data are available at Bioinformatics online.

引用

页码：2846 / 2847

页数：2

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