BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data.
BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data.
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DOI：
10.1186/s13073-018-0528-3
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发表时间：
2018-03-20
期刊：
影响因子：
12.3
通讯作者：
Bosinger SE
中科院分区：
文献类型：
--
作者：
Upadhyay AA;Kauffman RC;Wolabaugh AN;Cho A;Patel NB;Reiss SM;Havenar-Daughton C;Dawoud RA;Tharp GK;Sanz I;Pulendran B;Crotty S;Lee FE;Wrammert J;Bosinger SE
B细胞通过产生抗体在免疫反应中发挥关键作用，抗体表现出显著的多样性。在这里，我们描述了一个生物信息学管道，BALDR(使用从头重建的BCR谱系分配)，它从Illumina单细胞RNA-seq数据中准确地重建成对的重链和轻链免疫球蛋白基因序列。BaldR对人、恒河猴流感疫苗和猴免疫缺陷病毒疫苗诱导的成浆细胞以及幼稚和抗原特异性记忆B细胞的克隆型鉴定是准确的。BALDR使克隆类型识别与B细胞谱系中的单细胞转录信息相匹配，并将在疫苗、广泛中和抗体开发的人类免疫缺陷病毒和癌症领域有广泛的应用。BALDR的网址是：https://github.com/BosingerLab/BALDR.。本文的在线版本(10.1186/s13073-0180528-3)包含补充材料，可供授权用户使用。
B cells play a critical role in the immune response by producing antibodies, which display remarkable diversity. Here we describe a bioinformatic pipeline, BALDR (BCR Assignment of Lineage using De novo Reconstruction) that accurately reconstructs the paired heavy and light chain immunoglobulin gene sequences from Illumina single-cell RNA-seq data. BALDR was accurate for clonotype identification in human and rhesus macaque influenza vaccine and simian immunodeficiency virus vaccine induced vaccine-induced plasmablasts and naïve and antigen-specific memory B cells. BALDR enables matching of clonotype identity with single-cell transcriptional information in B cell lineages and will have broad application in the fields of vaccines, human immunodeficiency virus broadly neutralizing antibody development, and cancer. BALDR is available at https://github.com/BosingerLab/BALDR. The online version of this article (10.1186/s13073-018-0528-3) contains supplementary material, which is available to authorized users.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
46.9
作者：
Han, Arnold;Glanville, Jacob;Hansmann, Leo;Davis, Mark M.
通讯作者：
Davis, Mark M.
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
5.4
作者：
Kasturi, Sudhir Pai;Kozlowski, Pamela A.;Pulendran, Bali
通讯作者：
Pulendran, Bali
影响因子：
4
作者：
Eltahla, Auda A.;Rizzetto, Simone;Luciani, Fabio
通讯作者：
Luciani, Fabio