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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Abstract 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.
AbstractList 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.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.
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.
Author Shi, Yi
Hu, Yongfei
Liu, Peipei
Gao, George F
Zou, Jing
Zhao, Fangqing
Chen, Yan
Zhang, Ruifen
Wu, Jun
Lv, Na
Chen, Chen
Liu, Fei
Xiao, Xue
Zhu, Baoli
Liu, Di
Gao, Jing
Ma, Juncai
Yang, Xi
Liu, Jun
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  givenname: Yongfei
  surname: Hu
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  surname: Liu
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  organization: Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institutes of Life Sciences, Chinese Academy of Sciences, Beijing 100101, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China; and Chinese Center for Disease Control and Prevention, Beijing 102206, China zhubaoli@im.ac.cn gaof@im.ac.cn ma@im.ac.cn
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  givenname: Baoli
  surname: Zhu
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  email: zhubaoli@im.ac.cn, gaof@im.ac.cn, ma@im.ac.cn
  organization: Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China; and zhubaoli@im.ac.cn gaof@im.ac.cn ma@im.ac.cn
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Snippet The next-generation sequencing technology has promoted the study on human TCR repertoire, which is essential for the adaptive immunity. To decipher the...
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SubjectTerms 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
Title TCRklass: a new K-string-based algorithm for human and mouse TCR repertoire characterization
URI https://www.ncbi.nlm.nih.gov/pubmed/25404364
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