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Cell Immunol. 2014 Mar-Apr;288(1-2):31-8. doi: 10.1016/j.cellimm.2014.02.001. Epub 2014 Feb 23.

Qualifying high-throughput immune repertoire sequencing.

Author information

1
Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria. Electronic address: norbert.niklas@o.roteskreuz.at.
2
Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria. Electronic address: johannes.proell@o.roteskreuz.at.
3
Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria. Electronic address: johannes.weinberger@o.roteskreuz.at.
4
Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria. Electronic address: agnes.zopf@o.roteskreuz.at.
5
Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria. Electronic address: karin.wiesinger@o.roteskreuz.at.
6
University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria. Electronic address: konstantin.krismer@students.fh-hagenberg.at.
7
Division of Hematology/Oncology, Elisabethinen Hospital Linz, Fadingerstraße 1, 4020 Linz, Austria. Electronic address: peter@bettelheim.eu.
8
Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria. Electronic address: christian.gabriel@o.roteskreuz.at.

Abstract

Diversity of B and T cell receptors, achieved by gene recombination and somatic hypermutation, allows the immune system for recognition and targeted reaction against various threats. Next-generation sequencing for assessment of a cell's gene composition and variation makes deep analysis of one individual's immune spectrum feasible. An easy to apply but detailed analysis and visualization strategy is necessary to process all sequences generated. We performed sequencing utilizing the 454 system for CLL and control samples, utilized the IMGT database and applied the presented analysis tools. With the applied protocol, malignant clones are found and characterized, mutational status compared to germline identity is elaborated in detail showing that the CLL mutation status is not as monoclonal as generally thought. On the other hand, this strategy is not solely applicable to the 454 sequencing system but can easily be transferred to any other next-generation sequencing platform.

KEYWORDS:

Big data visualization; Clonotyping; Diversity generation; Immune repertoire; Immunoglobulin heavy chain; Next-generation sequencing; Somatic hypermutation; T cell receptor β; VDJ recombination

PMID:
24607567
DOI:
10.1016/j.cellimm.2014.02.001
[Indexed for MEDLINE]

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