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BMC Biotechnol. 2017 Jul 10;17(1):61. doi: 10.1186/s12896-017-0379-9.

Overview of methodologies for T-cell receptor repertoire analysis.

Author information

1
Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany.
2
Centre for Liver Research and NIHR Birmingham Liver Biomedical Research Unit, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK.
3
Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.
4
Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.
5
K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
6
Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
7
Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.
8
Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany. a.franke@mucosa.de.

Abstract

BACKGROUND:

The T-cell receptor (TCR), located on the surface of T cells, is responsible for the recognition of the antigen-major histocompatibility complex, leading to the initiation of an inflammatory response. Analysing the TCR repertoire may help to gain a better understanding of the immune system features and of the aetiology and progression of diseases, in particular those with unknown antigenic triggers. The extreme diversity of the TCR repertoire represents a major analytical challenge; this has led to the development of specialized methods which aim to characterize the TCR repertoire in-depth. Currently, next generation sequencing based technologies are most widely employed for the high-throughput analysis of the immune cell repertoire.

RESULTS:

Here, we report on the latest methodological advancements in the field by describing and comparing the available tools; from the choice of the starting material and library preparation method, to the sequencing technologies and data analysis. Finally, we provide a practical example and our own experience by reporting some exemplary results from a small internal benchmark study, where current approaches from the literature and the market are employed and compared.

CONCLUSIONS:

Several valid methods for clonotype identification and TCR repertoire analysis exist, however, a gold standard method for the field has not yet been identified. Depending on the purpose of the scientific study, some approaches may be more suitable than others. Finally, due to possible method specific biases, scientists must be careful when comparing results obtained using different methods.

KEYWORDS:

CDR3; Clonotype; Immune repertoire; Immunogenetics; Immunogenomics; T-cell receptor (TCR); TCR profiling; TCR repertoire; Target sequencing; Vdj

PMID:
28693542
PMCID:
PMC5504616
DOI:
10.1186/s12896-017-0379-9
[Indexed for MEDLINE]
Free PMC Article

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