National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg Germany.
Brief Bioinform. 2019 Jan 18;20(1):222-234. doi: 10.1093/bib/bbx111.
High-throughput sequencing technologies have exposed the possibilities for the in-depth evaluation of T-cell receptor (TCR) repertoires. These studies are highly relevant to gain insights into human adaptive immunity and to decipher the composition and diversity of antigen receptors in physiological and disease conditions. The major objective of TCR sequencing data analysis is the identification of V, D and J gene segments, complementarity-determining region 3 (CDR3) sequence extraction and clonality analysis. With the advancement in sequencing technologies, new TCR analysis approaches and programs have been developed. However, there is still a deficit of systematic comparative studies to assist in the selection of an optimal analysis approach. Here, we present a detailed comparison of 10 state-of-the-art TCR analysis tools on samples with different complexities by taking into account many aspects such as clonotype detection [unique V(D)J combination], CDR3 identification or accuracy in error correction. We used our in silico and experimental data sets with known clonalities enabling the identification of potential tool biases. We also established a new strategy, named clonal plane, which allows quantifying and comparing the clonality of multiple samples. Our results provide new insights into the effect of method selection on analysis results, and it will assist users in the selection of an appropriate analysis method.
高通量测序技术为深入评估 T 细胞受体 (TCR) 库提供了可能。这些研究对于深入了解人类适应性免疫以及解析生理和疾病条件下抗原受体的组成和多样性具有重要意义。TCR 测序数据分析的主要目标是鉴定 V、D 和 J 基因片段、互补决定区 3 (CDR3) 序列提取和克隆性分析。随着测序技术的进步，新的 TCR 分析方法和程序已经得到开发。然而，仍然缺乏系统的比较研究来协助选择最佳的分析方法。在这里，我们通过考虑许多方面，如克隆型检测（独特的 V(D)J 组合）、CDR3 识别或错误纠正的准确性，对 10 种最先进的 TCR 分析工具在不同复杂度的样本上进行了详细比较。我们使用具有已知克隆性的计算机模拟和实验数据集，能够识别潜在的工具偏差。我们还建立了一种新策略，称为克隆平面，它可以量化和比较多个样本的克隆性。我们的结果提供了对方法选择对分析结果的影响的新见解，并将帮助用户选择合适的分析方法。
