Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq.
Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq.
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DOI：
10.1186/s13073-016-0335-7
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发表时间：
2016-07-27
期刊：
影响因子：
12.3
通讯作者：
Elemento O
中科院分区：
文献类型：
--
作者：
Redmond D;Poran A;Elemento O
T细胞受体（TCR）α和β链库的准确表征对于理解适应性免疫至关重要。这种表征在疫苗开发和反应、癌症克隆跟踪和免疫治疗等领域有许多应用。在这里，我们提出了一种称为单细胞TCRseq（scTCRseq）的新方法，用于从配对末端单细胞RNA测序读取中识别和组装全长重排的V（D）J T细胞受体序列。该方法允许准确鉴定每个单个T细胞的V（D）J重排，并具有恢复成对α和β片段的新能力。源代码可在https://github.com/ElementoLab/scTCRseq上获得。本文的在线版本（doi：10.1186/s13073-016-0335-7）包含补充材料，可供授权用户使用。
Accurate characterization of the repertoire of the T-cell receptor (TCR) alpha and beta chains is critical to understanding adaptive immunity. Such characterization has many applications across such fields as vaccine development and response, clone-tracking in cancer, and immunotherapy. Here we present a new methodology called single-cell TCRseq (scTCRseq) for the identification and assembly of full-length rearranged V(D)J T-cell receptor sequences from paired-end single-cell RNA sequencing reads. The method allows accurate identification of the V(D)J rearrangements for each individual T-cell and has the novel ability to recover paired alpha and beta segments. Source code is available at https://github.com/ElementoLab/scTCRseq. The online version of this article (doi:10.1186/s13073-016-0335-7) contains supplementary material, which is available to authorized users.