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Stitchr: stitching coding TCR nucleotide sequences from V/J/CDR3 information.

James M Heather1,2, Matthew J Spindler3, Marta Herrero Alonso1

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Summary

Stitchr is a new software tool that generates full-length T cell receptor (TCR) coding sequences from minimal V/J/CDR3 information. This tool enhances the speed and reproducibility of TCR research and engineering.

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Area of Science:

  • Immunology
  • Bioinformatics
  • Molecular Biology

Background:

  • T cell receptors (TCRs) are crucial for immunology research.
  • Current methods often lack full-length coding sequences, hindering applications.
  • Existing TCR data is limited to V/J gene symbols and CDR3 amino acid sequences.

Purpose of the Study:

  • To introduce Stitchr, a software tool for generating complete TCR coding sequences.
  • To address the limitation of incomplete TCR sequence information in research.
  • To facilitate TCR engineering and manipulation.

Main Methods:

  • Stitchr software tool development.
  • Input: V/J gene symbols and CDR3 amino acid sequence.
  • Output: Full-length coding nucleotide sequences for TCR cDNA.
  • Validation through synthesis, transduction into Jurkat cells, and antigen specificity testing.
  • Companion script Thimble for high-throughput processing.

Main Results:

  • Stitchr successfully generates complete TCR coding sequences from minimal input.
  • Synthesized TCR sequences recapitulated parental antigen specificity in Jurkat cells.
  • The Thimble script processed one million TCRs in under ten minutes on a standard PC.

Conclusions:

  • Stitchr systematizes TCR sequence production and modification.
  • The tool is expected to increase the speed, repeatability, and reproducibility of TCR research.
  • Stitchr is available on GitHub for broader accessibility.