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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Veröffentlicht in:The Journal of immunology (1950) Jg. 194; H. 1; S. 446
Hauptverfasser: 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
Sprache:Englisch
Veröffentlicht: United States 01.01.2015
Schlagworte:
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
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Zusammenfassung: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.
Bibliographie:ObjectType-Article-2
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ISSN:1550-6606
1550-6606
DOI:10.4049/jimmunol.1400711