4.8 Article

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

期刊

NUCLEIC ACIDS RESEARCH
卷 50, 期 12, 页码 -

出版社

OXFORD UNIV PRESS
DOI: 10.1093/nar/gkac190

关键词

-

资金

  1. NIH/NCI [R01CA164273, R43CA232942]
  2. NIH/NIAID [R43AI12031301]
  3. Emily Venanzi Fund for Innovation in Lung Cancer Research
  4. Be a Piece of the Solution
  5. Targeting a Cure for Lung Cancer Research Fund at MGH (Boston, MA)

向作者/读者索取更多资源

The study and manipulation of T cell receptors (TCRs) are crucial in immunology research. Stitchr is a software tool that can generate complete TCR coding sequences based on minimal V/J/CDR3 information, increasing the speed and reproducibility of TCR research.
The study and manipulation of T cell receptors (TCRs) is central to multiple fields across basic and translational immunology research. Produced by V(D)J recombination, TCRs are often only recorded in the literature and data repositories as a combination of their V and J gene symbols, plus their hypervariable CDR3 amino acid sequence. However, numerous applications require full-length coding nucleotide sequences. Here we present Stitchr, a software tool developed to specifically address this limitation. Given minimal V/J/CDR3 information, Stitchr produces complete coding sequences representing a fully spliced TCR cDNA. Due to its modular design, Stitchr can be used for TCR engineering using either published germline or novel/modified variable and constant region sequences. Sequences produced by Stitchr were validated by synthesizing and transducing TCR sequences into Jurkat cells, recapitulating the expected antigen specificity of the parental TCR. Using a companion script, Thimble, we demonstrate that Stitchr can process a million TCRs in under ten minutes using a standard desktop personal computer. By systematizing the production and modification of TCR sequences, we propose that Stitchr will increase the speed, repeatability, and reproducibility of TCR research. Stitchr is available on GitHub.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.8
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

暂无数据
暂无数据