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Updated: Jan 29, 2026

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

Ida Lindeman1,2, Michael J T Stubbington3

  • 1Wellcome Sanger Institute, Hinxton, Cambridge, UK.

Methods in Molecular Biology (Clifton, N.J.)
|February 14, 2019
PubMed
Summary

TraCeR and BraCeR reconstruct paired full-length antigen receptor sequences and infer clonality from single-cell RNA-seq data. These computational tools aid in analyzing T-cell receptor (TCR) sequences and somatic hypermutations.

Keywords:
Antigen receptor reconstructionBCRBracerImmunoglobulinRNA-seqSingle cellTCRTracerscRNA-seq

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Area of Science:

  • Immunology
  • Bioinformatics
  • Computational Biology

Background:

  • Single-cell RNA sequencing (scRNA-seq) enables high-throughput analysis of individual cells.
  • Reconstructing antigen receptor sequences is crucial for understanding adaptive immune responses.
  • Accurate clonality inference requires robust computational methods.

Purpose of the Study:

  • To introduce TraCeR and BraCeR, computational tools for reconstructing antigen receptor sequences.
  • To enable clonality inference from scRNA-seq data.
  • To provide guidance on experimental design and results interpretation for these tools.

Main Methods:

  • TraCeR extracts TCR-derived reads from scRNA-seq data by aligning reads to synthetic TCR sequences.
  • Reconstructed TCR sequences are assembled into full-length recombined sequences.
  • BraCeR extends TraCeR by incorporating analysis of somatic hypermutations and isotype switching.

Main Results:

  • Successful reconstruction of paired full-length TCR sequences.
  • Accurate inference of immune cell clonality.
  • Demonstration of TraCeR and BraCeR utility in analyzing adaptive immune repertoires.

Conclusions:

  • TraCeR and BraCeR are valuable tools for scRNA-seq data analysis in immunology.
  • These tools facilitate detailed investigation of T-cell receptor repertoire.
  • The chapter provides a comprehensive guide for utilizing these computational methods.