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 accu...

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Bibliographic Details
Published in:	The Journal of immunology (1950) Vol. 194; no. 1; p. 446
Main Authors:	Yang, Xi, Liu, Di, Lv, Na, Zhao, Fangqing, Liu, Fei, Zou, Jing, Chen, Yan, Xiao, Xue, Wu, Jun, Liu, Peipei, Gao, Jing, Hu, Yongfei, Shi, Yi, Liu, Jun, Zhang, Ruifen, Chen, Chen, Ma, Juncai, Gao, George F, Zhu, Baoli
Format:	Journal Article
Language:	English
Published:	United States 01.01.2015
Subjects:	Algorithms Amino Acid Sequence Animals Automatic Data Processing - methods Base Sequence High-Throughput Nucleotide Sequencing - methods Humans Mice Molecular Sequence Data Receptors, Antigen, T-Cell - analysis Receptors, Antigen, T-Cell - genetics Receptors, Antigen, T-Cell - immunology Reproducibility of Results Sequence Analysis, DNA V(D)J Recombination - genetics
ISSN:	1550-6606, 1550-6606
Online Access:	Get more information
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Summary:	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.
Bibliography:	ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Undefined-1 ObjectType-Feature-3 content type line 23
ISSN:	1550-6606 1550-6606
DOI:	10.4049/jimmunol.1400711