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Medicine (Baltimore). 2016 Mar;95(10):e2839. doi: 10.1097/MD.0000000000002839.

High Throughput Sequencing of T Cell Antigen Receptors Reveals a Conserved TCR Repertoire.

Author information

1
From the 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 (XH, CL, QX, GC, JC, ZC, ZW, YD, PY, HD); Beijing Genomics Institute (SC); and Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital) (YD), Shenzhen, Guangdong, China.

Abstract

The T-cell receptor (TCR) repertoire is a mirror of the human immune system that reflects processes caused by infections, cancer, autoimmunity, and aging. Next-generation sequencing has become a powerful tool for deep TCR profiling. Herein, we used this technology to study the repertoire features of TCR beta chain in the blood of healthy individuals.Peripheral blood samples were collected from 10 healthy donors. T cells were isolated with anti-human CD3 magnetic beads according to the manufacturer's protocol. We then combined multiplex-PCR, Illumina sequencing, and IMGT/High V-QUEST to analyze the characteristics and polymorphisms of the TCR.Most of the individual T cell clones were present at very low frequencies, suggesting that they had not undergone clonal expansion. The usage frequencies of the TCR beta variable, beta joining, and beta diversity gene segments were similar among T cells from different individuals. Notably, the usage frequency of individual nucleotides and amino acids within complementarity-determining region (CDR3) intervals was remarkably consistent between individuals. Moreover, our data show that terminal deoxynucleotidyl transferase activity was biased toward the insertion of G (31.92%) and C (27.14%) over A (21.82%) and T (19.12%) nucleotides.Some conserved features could be observed in the composition of CDR3, which may inform future studies of human TCR gene recombination.

PMID:
26962778
PMCID:
PMC4998859
DOI:
10.1097/MD.0000000000002839
[Indexed for MEDLINE]
Free PMC Article

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