High-Throughput Sequencing of the T-Cell Receptor Beta Chain Gene Repertoire in Chronic Lymphocytic Leukemia

E Vlachonikola; A Vardi; K Stamatopoulos; A Hadzidimitriou

doi:10.1007/978-1-4939-8876-1_24

High-Throughput Sequencing of the T-Cell Receptor Beta Chain Gene Repertoire in Chronic Lymphocytic Leukemia

Methods Mol Biol. 2019:1881:355-363. doi: 10.1007/978-1-4939-8876-1_24.

Authors

E Vlachonikola^{1

2}, A Vardi^{1

3

4}, K Stamatopoulos^{1

4

5}, A Hadzidimitriou⁶

Affiliations

¹ Institute of Applied Biosciences (INAB), Center for Research and Technology (CERTH), Thessaloniki, Greece.
² Department of Genetics, Development and Molecular Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece.
³ HCT Unit, Hematology Department, G. Papanikolaou Hospital, Thessaloniki, Greece.
⁴ Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
⁵ Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
⁶ Institute of Applied Biosciences (INAB), Center for Research and Technology (CERTH), Thessaloniki, Greece. anastasiaxtz@gmail.com.

PMID: 30350216
DOI: 10.1007/978-1-4939-8876-1_24

Abstract

High-throughput, next-generation sequencing (NGS) offers a unique opportunity for in-depth characterization of adaptive immune receptor repertoires. Nevertheless, limitations and pitfalls exist in every step of both the experimental and the analytical procedure, leading to discrepancies in the literature and incomprehensive and/or altogether misleading results. Thus, standardization of protocols in NGS immunogenetics is urgently needed.Here, we describe the experimental protocol that we developed for T-cell receptor beta chain (TRB) gene repertoire analysis in chronic lymphocytic leukemia, aiming to provide a reproducible and biologically meaningful output. Although optimized for TRBV-TRBD-TRBJ gene rearrangements, this protocol may be customized for other adaptive immune receptor sequences, as well.

Keywords: CLL; Next-generation sequencing; TR.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods
Gene Rearrangement
Genome, Human*
High-Throughput Nucleotide Sequencing / methods*
Humans
Immunogenetics
Leukemia, Lymphocytic, Chronic, B-Cell / genetics*
Receptors, Antigen, T-Cell, alpha-beta / genetics*
Sequence Analysis, DNA / methods*
Software

Substances

Receptors, Antigen, T-Cell, alpha-beta