Evaluation of the capacities of mouse TCR profiling from short read RNA-seq data.
Evaluation of the capacities of mouse TCR profiling from short read RNA-seq data.
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DOI：
10.1371/journal.pone.0207020
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发表时间：
2018
期刊：
影响因子：
3.7
通讯作者：
Fury W
中科院分区：
文献类型：
--
作者：
Bai Y;Wang D;Li W;Huang Y;Ye X;Waite J;Barry T;Edelmann KH;Levenkova N;Guo C;Skokos D;Wei Y;Macdonald LE;Fury W
通过短读转录组测序（RNA- seq）分析T细胞受体（TCR）库具有同时探测TCR和其他基因的全基因组RNA表达的独特优势。然而，与靶向扩增子方法相比，较短的读取长度更容易产生映射错误。此外，只有很小比例的全基因组读数可能覆盖TCR位点，因此，该曲目可能明显不足采样。尽管这种方法已在一些研究中得到应用，但转录组测序在探测TCR谱中的效用尚未得到广泛评估。在这里，我们提出了一个系统的评估RNA-Seq在TCR分析。我们评估了Fluidigm C1全长单细胞RNA-Seq和散装RNA-Seq在naïve条件下或免疫原性挑战后表征不同多样性的能力。我们采用标准的读长和测序覆盖率，以便按照当前的RNA-Seq惯例进行评估。尽管大量RNA-Seq的测序深度很高，但我们在量化转录物丰度低（<1%）的tcr时遇到了困难。然而，丰度为1-3%或更高的顶级富集tcr可以被忠实地检测和量化。当对顶级TCR序列感兴趣并且转录组测序可用时，使用RNA-Seq数据进行TCR分析是值得的。
Profiling T cell receptor (TCR) repertoire via short read transcriptome sequencing (RNA-Seq) has a unique advantage of probing simultaneously TCRs and the genome-wide RNA expression of other genes. However, compared to targeted amplicon approaches, the shorter read length is more prone to mapping error. In addition, only a small percentage of the genome-wide reads may cover the TCR loci and thus the repertoire could be significantly under-sampled. Although this approach has been applied in a few studies, the utility of transcriptome sequencing in probing TCR repertoires has not been evaluated extensively. Here we present a systematic assessment of RNA-Seq in TCR profiling. We evaluate the power of both Fluidigm C1 full-length single cell RNA-Seq and bulk RNA-Seq in characterizing the repertoires of different diversities under either naïve conditions or after immunogenic challenges. Standard read length and sequencing coverage were employed so that the evaluation was conducted in accord with the current RNA-Seq practices. Despite high sequencing depth in bulk RNA-Seq, we encountered difficulty quantifying TCRs with low transcript abundance (<1%). Nevertheless, top enriched TCRs with an abundance of 1–3% or higher can be faithfully detected and quantified. When top TCR sequences are of interest and transcriptome sequencing is available, it is worthwhile to conduct a TCR profiling using the RNA-Seq data.
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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：
56.9
作者：
Arstila, TP;Casrouge, A;Kourilsky, P
通讯作者：
Kourilsky, P
DOI：
10.1186/1742-4933-9-17
发表时间：
2012-08-15
期刊：
Immunity & ageing : I & A
影响因子：
--
作者：
Bunztman A;Vincent BG;Krovi H;Steele S;Frelinger JA
通讯作者：
Frelinger JA
影响因子：
17.1
作者：
Howie, Bryan;Sherwood, Anna M.;Robins, Harlan S.
通讯作者：
Robins, Harlan S.
DOI：
10.1093/cid/ciw767
发表时间：
2017-02-15
期刊：
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
影响因子：
--
作者：
Bouquet J;Gardy JL;Brown S;Pfeil J;Miller RR;Morshed M;Avina-Zubieta A;Shojania K;McCabe M;Parker S;Uyaguari M;Federman S;Tang P;Steiner T;Otterstater M;Holt R;Moore R;Chiu CY;Patrick DM;Complex Chronic Disease Study Group
通讯作者：
Complex Chronic Disease Study Group