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

  • E. Vlachonikola
  • A. Vardi
  • K. Stamatopoulos
  • A. Hadzidimitriou
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1881)

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.

Key words

TR CLL Next-generation sequencing 

Notes

Financial Support

Supported in part by H2020 “AEGLE, An analytics framework for integrated and personalized healthcare services in Europe”, by the EU; “MEDGENET, Medical Genomics and Epigenomics Network” (No.692298) by the EU.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • E. Vlachonikola
    • 1
    • 2
  • A. Vardi
    • 1
    • 3
    • 4
  • K. Stamatopoulos
    • 1
    • 4
    • 5
  • A. Hadzidimitriou
    • 1
  1. 1.Institute of Applied Biosciences (INAB), Center for Research and Technology (CERTH)ThessalonikiGreece
  2. 2.Department of Genetics, Development and Molecular BiologyAristotle University of ThessalonikiThessalonikiGreece
  3. 3.HCT Unit, Hematology DepartmentG. Papanikolaou HospitalThessalonikiGreece
  4. 4.Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
  5. 5.Department of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden

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