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J Immunol. 2017 May 15;198(10):3765-3774. doi: 10.4049/jimmunol.1602050. Epub 2017 Apr 17.

High-Throughput Immunogenetics for Clinical and Research Applications in Immunohematology: Potential and Challenges.

Author information

1
Department of Immunology, Laboratory for Medical Immunology, Erasmus MC, University Medical Center, 3015 CN Rotterdam, the Netherlands; a.langerak@erasmusmc.nl.
2
Second Medical Department, University Hospital Schleswig-Holstein, 24105 Kiel, Germany.
3
Département d'Hématologie, Assistance Publique - Hôpitaux de Paris Hopital Pitié-Salpêtrière and Université Pierre et Marie Curie - Université Paris IV, 75005 Paris, France.
4
Molecular Medicine Program, Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic.
5
Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast BT9 7AE, United Kingdom.
6
Centro Ricerca Tettamanti, Clinica Pediatrica Università Milano-Bicocca, 20900 Monza, Italy.
7
UMR 9002 CNRS - Université de Montpellier, 34396 Montpellier, France.
8
Centre de Recherche en Informatique Signal et Automatique de Lille, CNRS, Université de Lille, 59000 Lille, France.
9
Département d'Hématologie, Assistance Publique - Hôpitaux de Paris Necker-Enfants Malades and Paris Descartes, 75015 Paris, France.
10
Institut für Pathologie, Charité - Universitätsmedizin Berlin, D-10117 Berlin, Germany.
11
Department of Pathology, Radboud University Nijmegen Medical Center, 6525 GA Nijmegen, the Netherlands; and.
12
Institute of Applied Biosciences, Center for Research and Technology Hellas, GR-57001 Thessaloniki, Greece.

Abstract

Analysis and interpretation of Ig and TCR gene rearrangements in the conventional, low-throughput way have their limitations in terms of resolution, coverage, and biases. With the advent of high-throughput, next-generation sequencing (NGS) technologies, a deeper analysis of Ig and/or TCR (IG/TR) gene rearrangements is now within reach, which impacts on all main applications of IG/TR immunogenetic analysis. To bridge the generation gap from low- to high-throughput analysis, the EuroClonality-NGS Consortium has been formed, with the main objectives to develop, standardize, and validate the entire workflow of IG/TR NGS assays for 1) clonality assessment, 2) minimal residual disease detection, and 3) repertoire analysis. This concerns the preanalytical (sample preparation, target choice), analytical (amplification, NGS), and postanalytical (immunoinformatics) phases. Here we critically discuss pitfalls and challenges of IG/TR NGS methodology and its applications in hemato-oncology and immunology.

PMID:
28416603
DOI:
10.4049/jimmunol.1602050
[Indexed for MEDLINE]
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