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

  • Ida Lindeman
  • Michael J. T. Stubbington
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

TCR BCR Immunoglobulin Single cell RNA-seq scRNA-seq Antigen receptor reconstruction Tracer Bracer 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Ida Lindeman
    • 1
    • 2
  • Michael J. T. Stubbington
    • 1
  1. 1.Wellcome Sanger InstituteHinxton, CambridgeUK
  2. 2.KG Jebsen Coeliac Disease Research Centre and Department of ImmunologyUniversity of OsloOsloNorway

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