Immunoglobulin/T-Cell Receptor Gene Rearrangement Analysis Using RNA-Seq

Vincent H J van der Velden; Lorenz Bastian; Monika Brüggemann; Alina M Hartmann; Nikos Darzentas

doi:10.1007/978-1-0716-2115-8_4

Immunoglobulin/T-Cell Receptor Gene Rearrangement Analysis Using RNA-Seq

Methods Mol Biol. 2022:2453:61-77. doi: 10.1007/978-1-0716-2115-8_4.

Authors

Vincent H J van der Velden¹, Lorenz Bastian², Monika Brüggemann², Alina M Hartmann², Nikos Darzentas²

Affiliations

¹ Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands. v.h.j.vandervelden@erasmusmc.nl.
² Department of Hematology, University of Schleswig-Holstein, Kiel, Germany.

Abstract

Identification of immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements in acute lymphoblastic leukemia (ALL) patients at initial presentation are crucial for monitoring of minimal residual disease (MRD) during subsequent follow-up and thereby for appropriate risk-group stratification. Here we describe how RNA-Seq data can be generated and subsequently analyzed with ARResT/Interrogate to identify possible MRD markers. In addition to the procedures, possible pitfalls will be discussed. Similar strategies can be employed for other lymphoid malignancies, such as lymphoma and myeloma.

Keywords: Acute lymphoblastic leukemia; Gene rearrangements; Immunoglobulin; Marker identification; Minimal residual disease; RNA-Seq; T-cell receptor; Whole exome sequencing; Whole genome sequencing.

MeSH terms

Aftercare
Gene Rearrangement* / genetics
Genes, T-Cell Receptor* / genetics
Humans
Immunoglobulins* / genetics
Neoplasm, Residual* / genetics
Precursor Cell Lymphoblastic Leukemia-Lymphoma* / genetics
RNA-Seq* / methods
Risk Assessment

Substances

Immunoglobulins