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Antigen Receptor Sequence Reconstruction and Clonality Inference from scRNA-Seq Data

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Computational Methods for Single-Cell Data Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1935))

Abstract

In this chapter, we describe TraCeR and BraCeR, our computational tools for reconstruction of paired full-length antigen receptor sequences and clonality inference from single-cell RNA-seq (scRNA-seq) data. In brief, TraCeR reconstructs T-cell receptor (TCR) sequences from scRNA-seq data by extracting sequencing reads derived from TCRs by aligning the reads from each cell against synthetic TCR sequences. TCR-derived reads are then assembled into full-length recombined TCR sequences. BraCeR builds on the TraCeR pipeline and accounts for somatic hypermutations (SHM) and isotype switching. Here we discuss experimental design, use of the tools, and interpretation of the results.

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Authors and Affiliations

  1. Wellcome Sanger Institute, Hinxton, Cambridge, UK

    Ida Lindeman & Michael J. T. Stubbington

  2. KG Jebsen Coeliac Disease Research Centre and Department of Immunology, University of Oslo, Oslo, Norway

    Ida Lindeman

Authors
  1. Ida Lindeman
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  2. Michael J. T. Stubbington
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Editors and Affiliations

  1. Dana–Farber Cancer Institute and Harvard Chan, School of Public Health, Boston, MA, USA

    Guo-Cheng Yuan

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Lindeman, I., Stubbington, M.J.T. (2019). Antigen Receptor Sequence Reconstruction and Clonality Inference from scRNA-Seq Data. In: Yuan, GC. (eds) Computational Methods for Single-Cell Data Analysis. Methods in Molecular Biology, vol 1935. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9057-3_15

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  • DOI: https://doi.org/10.1007/978-1-4939-9057-3_15

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