Tools for fundamental analysis functions of TCR repertoires: a systematic comparison.

The full set of T cell receptors (TCRs) in an individual is known as his or her TCR repertoire. Defining TCR repertoires under physiological conditions and in response to a disease or vaccine may lead to a better understanding of adaptive immunity and thus has great biological and clinical value. In the past decade, several high-throughput sequencing-based tools have been developed to assign TCRs to germline genes and to extract complementarity-determining region 3 (CDR3) sequences using different algorithms. Although these tools claim to be able to perform the full range of fundamental TCR repertoire analyses, there is no clear consensus of which tool is best suited to particular projects. Here, we present a systematic analysis of 12 available TCR repertoire analysis tools using simulated data, with an emphasis on fundamental analysis functions. Our results shed light on the detailed functions of TCR repertoire analysis tools and may therefore help researchers in the field to choose the right tools for their particular experimental design.

Zhang Y ，Yang X ，Zhang Y ，Zhang Y ，Wang M ，Ou JX ，Zhu Y ，Zeng H ，Wu J ，Lan C ，Zhou HW ，Yang W ，Zhang Z ... -  《-》

Computational Analysis of T-Cell Receptor Repertoire Workflow: From T-Cell Isolation to Bioinformatics Analysis.

The T-cell receptor (TCR) is the key molecule involved in the adaptive immune response. It is generated by the V(D)J recombination, responsible of the enormous diversity of the TCR repertoire, a crucial feature determining the individual capability to response to antigens and to build immunological memory. A pivotal role in the recognition of antigen is played by the hypervariable complementarity-determining region 3 (CDR3) of the V-beta chain of TCR. Investigating the CDR3 supports the understanding of the adaptive immune system dynamics in physiological processes, such as immune aging, and in disease, especially autoimmune disorders in which T cells are main actors. High-throughput sequencing (HTS) paved the way for a great progress in the investigation of TCR repertoire, enhancing the read depth in the process of library generation of sequencing and the number of samples that can be analyzed simultaneously. Therefore, the leverage of big datasets stressed the need to develop computational approach, by bioinformatics, to unravel the characteristics of the TCR repertoire.

Amoriello R ，Maghrebi O ，Ballerini C 《-》

Molecular constraints on CDR3 for thymic selection of MHC-restricted TCRs from a random pre-selection repertoire.

Lu J ，Van Laethem F ，Bhattacharya A ，Craveiro M ，Saba I ，Chu J ，Love NC ，Tikhonova A ，Radaev S ，Sun X ，Ko A ，Arnon T ，Shifrut E ，Friedman N ，Weng NP ，Singer A ，Sun PD ... -  《Nature Communications》

TCRklass: a new K-string-based algorithm for human and mouse TCR repertoire characterization.

The next-generation sequencing technology has promoted the study on human TCR repertoire, which is essential for the adaptive immunity. To decipher the complexity of TCR repertoire, we developed an integrated pipeline, TCRklass, using K-string-based algorithm that has significantly improved the accuracy and performance over existing tools. We tested TCRklass using manually curated short read datasets in comparison with in silico datasets; it showed higher precision and recall rates on CDR3 identification. We applied TCRklass on large datasets of two human and three mouse TCR repertoires; it demonstrated higher reliability on CDR3 identification and much less biased V/J profiling, which are the two components contributing the diversity of the repertoire. Because of the sequencing cost, short paired-end reads generated by next-generation sequencing technology are and will remain the main source of data, and we believe that the TCRklass is a useful and reliable toolkit for TCR repertoire analysis.

Yang X ，Liu D ，Lv N ，Zhao F ，Liu F ，Zou J ，Chen Y ，Xiao X ，Wu J ，Liu P ，Gao J ，Hu Y ，Shi Y ，Liu J ，Zhang R ，Chen C ，Ma J ，Gao GF ，Zhu B ... -  《-》

Analysis of the Repertoire Features of TCR Beta Chain CDR3 in Human by High-Throughput Sequencing.

To ward off a wide variety of pathogens, the human adaptive immune system harbors a vast array of T-cell receptors, collectively referred to as the TCR repertoire. Assessment of the repertoire features of TCR is vital for us to deeper understand of immune behaviour and immune response. In this study, we used a combination of multiplex-PCR, Illumina sequencing and IMGT (ImMunoGeneTics)/HighV-QUEST for a standardized analysis of the repertoire features of TCR beta chain in the blood of healthy individuals, including the repertoire features of public TCR complementarity-determining regions (CDR3) sequences, highly expanded clones, long TCR CDR3 sequences. We found that public CDR3 sequences and high-frequency sequences had the same characteristics, both of them had fewer nucleotide additions and shorter CDR3 length, which were closer to the germline sequence. Moreover, our studies provided evidence that public amino acid sequences are produced by multiple nucleotide sequences. Notably, there was skewed VDJ segment usage in long CDR3 sequences, the expression levels of 10 TRβV segments, 7 TRβJ segments and 2 TRβD segments were significantly different in the long CDR3 sequences compared to the short CDR3 sequences. Moreover, we identified that extensive N additions and increase of D gene usage contributing to TCR CDR3 length, and observed there was distinct usage frequency of amino acids in long CDR3 sequences compared to the short CDR3 sequences. Some repertoire features could be observed in the public sequences, highly abundance clones, and long TCR CDR3 sequences, which might be helpful for further study of immune behavior and immune response.

Hou X ，Wang M ，Lu C ，Xie Q ，Cui G ，Chen J ，Du Y ，Dai Y ，Diao H ... -  《-》