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Can We Detect T Cell Receptors from Long-Read RNA-Seq Data?

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Bioinformatics and Biomedical Engineering (IWBBIO 2022)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 13347))

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Abstract

T cells play an essential role in defense of the organism against pathogens and cancer. Efficient protection requires a vast repertoire of immune receptors, which is created by the V(D)J recombination process. There are multiple algorithms designed for the annotation of recombined T cell receptor (TR) sequences from traditional (short-read) RNA-Seq, however, none is adjusted for the long-read data. Here we intend to examine whether existing methods for TR sequences annotation using traditional RNA-Seq can be utilized for long-read sequencing data. ImReP, TRUST4, CATT and MiXCR algorithms were applied to data obtained by nanopore technology (PromethION). Adjustment of parameters was performed. The biggest number of CDR3 sequences was detected by the TRUST4 algorithm (20,599 unique TR sequences out of 73,904,478 total reads), representing 25% of the expected number of sequences. The distribution of annotated V and J genes was the same for MiXCR and TRUST4 algorithms and may be used to analyze the repertoire of V/J gene used in rearranged TR genes. Due to the high sequencing error rate of the analyzed sample (median read quality Q = 6.9), TR clonotype analysis is not suggested, and additional error correction steps are recommended for such analyses.

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Acknowledgment

This work was funded by the European Social Fund grant POWR.03.02.00–00-I029 and by the Silesian University of Technology grant for Support and Development of Research Potential.

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Authors and Affiliations

  1. Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland

    Justyna Mika & Joanna Polanska

  2. Laboratoire de Chimie Et Biologie Des Métaux, Université Grenoble Alpes, CNRS, CEA, 38000, Grenoble, France

    Serge M. Candéias

  3. Cancer Mechanisms and Biomarkers Group, Radiation Effects Department, Radiation Chemical & Environmental Hazards, UK Health Security Agency, Didcot, UK

    Christophe Badie

Authors
  1. Justyna Mika
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  2. Serge M. Candéias
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  3. Christophe Badie
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  4. Joanna Polanska
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Corresponding authors

Correspondence to Justyna Mika or Joanna Polanska .

Editor information

Editors and Affiliations

  1. Marcelina Siebold Guest Relations Dept., University of Granada, Granada, Spain

    Ignacio Rojas

  2. Faculty of Sciences, University of Granada, Granada, Spain

    Olga Valenzuela

  3. ETSIIT. CITIC-UGR, University of Granada, Granada, Spain

    Fernando Rojas

  4. ETSIIT, University of Granada, Granada, Spain

    Luis Javier Herrera

  5. University of Granada, Granada, Spain

    Francisco Ortuño

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Mika, J., Candéias, S.M., Badie, C., Polanska, J. (2022). Can We Detect T Cell Receptors from Long-Read RNA-Seq Data?. In: Rojas, I., Valenzuela, O., Rojas, F., Herrera, L.J., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2022. Lecture Notes in Computer Science(), vol 13347. Springer, Cham. https://doi.org/10.1007/978-3-031-07802-6_38

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  • DOI: https://doi.org/10.1007/978-3-031-07802-6_38

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-031-07801-9

  • Online ISBN: 978-3-031-07802-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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