title: Analysis of the Repertoire Features of TCR Beta Chain CDR3 in Human by High-Throughput Sequencing.
abstract: OBJECTIVE
  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.
  
  
  METHODS
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
authors.forename: Xianliang
authors.initials: X
authors.lastname: Hou
authors.forename: Mingbang
authors.initials: M
authors.lastname: Wang
authors.forename: Chong
authors.initials: C
authors.lastname: Lu
authors.forename: Qian
authors.initials: Q
authors.lastname: Xie
authors.forename: Guangying
authors.initials: G
authors.lastname: Cui
authors.forename: Jianing
authors.initials: J
authors.lastname: Chen
authors.forename: Yu
authors.initials: Y
authors.lastname: Du
authors.forename: Yong
authors.initials: Y
authors.lastname: Dai
authors.forename: Hongyan
authors.initials: H
authors.lastname: Diao
mesh_terms: D000328:Adult; D000595:Amino Acid Sequence; D001483:Base Sequence; D022801:Complementarity Determining Regions / Q000235:genetics* / Q000276:immunology; D030541:Databases, Genetic; D005260:Female; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D008875:Middle Aged; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods*; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000235:genetics* / Q000276:immunology; D013601:T-Lymphocytes / Q000378:metabolism; D055815:Young Adult
chemical_list: D022801:Complementarity Determining Regions; D016693:Receptors, Antigen, T-Cell, alpha-beta