Nanopore Sequencing for T-Cell Receptor Rearrangement Analysis in Cutaneous T-Cell Lymphoma

Cieslak C, Hain C, Rückert-Reed C, Busche T, Klages LJ, Schaper-Gerhardt K, Gutzmer R, Kalinowski J, Stadler R (2024)
Cancers 16(21): 3700.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Cieslak, Cassandra; Hain, CarstenUniBi; Rückert-Reed, ChristianUniBi ; Busche, TobiasUniBi; Klages, Levin JoeUniBi ; Schaper-Gerhardt, Katrin; Gutzmer, Ralf; Kalinowski, JörnUniBi; Stadler, Rudolf
Abstract / Bemerkung
Background: Analysis of T-cell receptor (TCR) clonality is a major diagnostic tool for lymphomas, particularly for cutaneous T-cell lymphomas (CTCL) like Mycosis fungoides and Sézary syndrome. However, a fast and cost-effective workflow is needed to enable widespread use of this method. Methods: We established a procedure for TCR rearrangement analysis via Oxford Nanopore Technology (ONT) sequencing. TCR receptor rearrangements (TCR-gamma and TCR-beta chains) were analyzed in samples from 45 patients with various diagnoses: Mycosis fungoides (37/45), Sézary Syndrome (2/45), folliculotropic CTCL (1/45), and non-CTCL diagnoses as polyclonal controls (5/45). Sample types included formalin-fixed paraffin-embedded (FFPE) samples (27/45), fresh frozen samples (9/45), and CD3-isolated cells (9/45). In addition, DNA of a Jurkat cell line was used as a monoclonal control. TCR amplicons were generated employing an optimized version of the protocol from the Euro Clonality consortium. Sequencing was conducted on the ONT GridION and Illumina MiSeq platforms, followed by similar bioinformatic analysis protocols. The tumor clone frequency (TCF), a crucial prognostic factor for CTCL patients, was used for method comparison. Results: The use of an optimized amplicon protocol and adapted bioinformatic tools demonstrated a strong correlation in TCF values between both sequencing methods across all sample types (range R: 0.992–0.996; range r2: 0.984–0.991). Conclusions: In summary, ONT sequencing was able to detect TCR clonality comparable to NGS, indicating its potential as a faster and more cost-effective option for routine diagnostic use.
Erscheinungsjahr
2024
Zeitschriftentitel
Cancers
Band
16
Ausgabe
21
Art.-Nr.
3700
eISSN
2072-6694
Page URI
https://pub.uni-bielefeld.de/record/2993996

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Cieslak C, Hain C, Rückert-Reed C, et al. Nanopore Sequencing for T-Cell Receptor Rearrangement Analysis in Cutaneous T-Cell Lymphoma. Cancers. 2024;16(21): 3700.
Cieslak, C., Hain, C., Rückert-Reed, C., Busche, T., Klages, L. J., Schaper-Gerhardt, K., Gutzmer, R., et al. (2024). Nanopore Sequencing for T-Cell Receptor Rearrangement Analysis in Cutaneous T-Cell Lymphoma. Cancers, 16(21), 3700. https://doi.org/10.3390/cancers16213700
Cieslak, Cassandra, Hain, Carsten, Rückert-Reed, Christian, Busche, Tobias, Klages, Levin Joe, Schaper-Gerhardt, Katrin, Gutzmer, Ralf, Kalinowski, Jörn, and Stadler, Rudolf. 2024. “Nanopore Sequencing for T-Cell Receptor Rearrangement Analysis in Cutaneous T-Cell Lymphoma”. Cancers 16 (21): 3700.
Cieslak, C., Hain, C., Rückert-Reed, C., Busche, T., Klages, L. J., Schaper-Gerhardt, K., Gutzmer, R., Kalinowski, J., and Stadler, R. (2024). Nanopore Sequencing for T-Cell Receptor Rearrangement Analysis in Cutaneous T-Cell Lymphoma. Cancers 16:3700.
Cieslak, C., et al., 2024. Nanopore Sequencing for T-Cell Receptor Rearrangement Analysis in Cutaneous T-Cell Lymphoma. Cancers, 16(21): 3700.
C. Cieslak, et al., “Nanopore Sequencing for T-Cell Receptor Rearrangement Analysis in Cutaneous T-Cell Lymphoma”, Cancers, vol. 16, 2024, : 3700.
Cieslak, C., Hain, C., Rückert-Reed, C., Busche, T., Klages, L.J., Schaper-Gerhardt, K., Gutzmer, R., Kalinowski, J., Stadler, R.: Nanopore Sequencing for T-Cell Receptor Rearrangement Analysis in Cutaneous T-Cell Lymphoma. Cancers. 16, : 3700 (2024).
Cieslak, Cassandra, Hain, Carsten, Rückert-Reed, Christian, Busche, Tobias, Klages, Levin Joe, Schaper-Gerhardt, Katrin, Gutzmer, Ralf, Kalinowski, Jörn, and Stadler, Rudolf. “Nanopore Sequencing for T-Cell Receptor Rearrangement Analysis in Cutaneous T-Cell Lymphoma”. Cancers 16.21 (2024): 3700.
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2024-11-04T07:11:55Z
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