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.

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