{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:34:04Z","timestamp":1760146444518,"version":"build-2065373602"},"reference-count":44,"publisher":"MDPI AG","issue":"21","license":[{"start":{"date-parts":[[2024,11,1]],"date-time":"2024-11-01T00:00:00Z","timestamp":1730419200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cancers"],"abstract":"<jats:p>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 S\u00e9zary 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), S\u00e9zary 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\u20130.996; range r2: 0.984\u20130.991). 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.<\/jats:p>","DOI":"10.3390\/cancers16213700","type":"journal-article","created":{"date-parts":[[2024,11,1]],"date-time":"2024-11-01T04:59:54Z","timestamp":1730437194000},"page":"3700","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Nanopore Sequencing for T-Cell Receptor Rearrangement Analysis in Cutaneous T-Cell Lymphoma"],"prefix":"10.3390","volume":"16","author":[{"given":"Cassandra","family":"Cieslak","sequence":"first","affiliation":[{"name":"Department of Dermatology, Johannes Wesling Medical Centre, University Hospitals of the Ruhr-University of Bochum (UKRUB), University of Bochum, 32429 Minden, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carsten","family":"Hain","sequence":"additional","affiliation":[{"name":"Medical School OWL, Bielefeld University, 33594 Bielefeld, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9722-4435","authenticated-orcid":false,"given":"Christian","family":"R\u00fcckert-Reed","sequence":"additional","affiliation":[{"name":"Medical School OWL, Bielefeld University, 33594 Bielefeld, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9211-8927","authenticated-orcid":false,"given":"Tobias","family":"Busche","sequence":"additional","affiliation":[{"name":"Medical School OWL, Bielefeld University, 33594 Bielefeld, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Levin Joe","family":"Klages","sequence":"additional","affiliation":[{"name":"Medical School OWL, Bielefeld University, 33594 Bielefeld, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katrin","family":"Schaper-Gerhardt","sequence":"additional","affiliation":[{"name":"Department of Dermatology, Johannes Wesling Medical Centre, University Hospitals of the Ruhr-University of Bochum (UKRUB), University of Bochum, 32429 Minden, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7921-2820","authenticated-orcid":false,"given":"Ralf","family":"Gutzmer","sequence":"additional","affiliation":[{"name":"Department of Dermatology, Johannes Wesling Medical Centre, University Hospitals of the Ruhr-University of Bochum (UKRUB), University of Bochum, 32429 Minden, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9052-1998","authenticated-orcid":false,"given":"J\u00f6rn","family":"Kalinowski","sequence":"additional","affiliation":[{"name":"Medical School OWL, Bielefeld University, 33594 Bielefeld, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2683-6028","authenticated-orcid":false,"given":"Rudolf","family":"Stadler","sequence":"additional","affiliation":[{"name":"Department of Dermatology, Johannes Wesling Medical Centre, University Hospitals of the Ruhr-University of Bochum (UKRUB), University of Bochum, 32429 Minden, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,11,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1016\/j.jaad.2016.03.009","article-title":"New Insights into Folliculotropic Mycosis Fungoides (FMF): A Single-Center Experience","volume":"75","author":"Hodak","year":"2016","journal-title":"J. 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