IMonitor: A Robust Pipeline for TCR and BCR Repertoire Analysis
IMonitor: A Robust Pipeline for TCR and BCR Repertoire Analysis
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DOI：
10.1534/genetics.115.176735
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发表时间：
2015-10-01
期刊：
影响因子：
3.3
通讯作者：
Liu, Xiao
中科院分区：
文献类型：
--
作者：
Zhang, Wei;Du, Yuanping;Liu, Xiao
下一代测序（NGS）技术的进步为通过对T细胞受体（TCR）和B细胞受体（BCR）进行深度测序来探测免疫库的巨大多样性提供了前所未有的机会。然而，仍然需要一个高效准确的分析工具来处理大量的数据。我们开发了一个高分辨率的分析管道，免疫监测器（IMonitor）来解决这一任务。该方法在共同的局部比对之后利用重新比对来鉴定V（D）J基因和等位基因。通过模拟序列和公开序列的重排，将IMonitor与其他工具进行了比较，证明了IMonitor在多方面的上级性能。与此同时，开发了一种方法来纠正PCR和测序错误，并最大限度地减少不同的V和J基因家族的各种重排序列之间的PCR偏倚。IMonitor提供了来自不同物种的所有受体链的序列的一般适应，并输出有用的统计数据和可视化。在本文的最后部分，我们展示了它在B细胞急性淋巴细胞白血病患者微小残留病检测中的应用。总之，该软件包将广泛用于免疫库分析。
The advance of next generation sequencing (NGS) techniques provides an unprecedented opportunity to probe the enormous diversity of the immune repertoire by deep sequencing T-cell receptors (TCRs) and B-cell receptors (BCRs). However, an efficient and accurate analytical tool is still on demand to process the huge amount of data. We have developed a high-resolution analytical pipeline, Immune Monitor (IMonitor) to tackle this task. This method utilizes realignment to identify V(D)J genes and alleles after common local alignment. We compare IMonitor with other published tools by simulated and public rearranged sequences, and it demonstrates its superior performance in most aspects. Together with this, a methodology is developed to correct the PCR and sequencing errors and to minimize the PCR bias among various rearranged sequences with different V and J gene families. IMonitor provides general adaptation for sequences from all receptor chains of different species and outputs useful statistics and visualizations. In the final part of this article, we demonstrate its application on minimal residual disease detection in patients with B-cell acute lymphoblastic leukemia. In summary, this package would be of widespread usage for immune repertoire analysis.