Stitchr

Stitchr reconstructs full-length coding nucleotide sequences of T cell receptors (TCRs) from variable (V) and joining (J) gene symbols together with CDR3 amino acid sequences to produce fully spliced TCR cDNA for downstream analyses and engineering.

Key Features:

• Input reconstruction: Reconstructs coding nucleotide sequences from V/J gene symbols and CDR3 amino acid sequences.
• cDNA assembly: Generates fully spliced TCR cDNA sequences by assembling variable, joining, CDR3, and constant region components.
• Germline and user sequences: Accepts published germline sequences or user-provided novel or modified variable and constant region sequences.
• Experimental validation: Synthesized and transduced sequences into Jurkat cells reproduced original antigen specificity.
• High-throughput processing: Companion script Thimble enables processing of up to one million TCRs in under ten minutes on a standard desktop.
• Modular design: Employs a modular architecture to generate and modify TCR sequence segments.

Scientific Applications:

• TCR engineering: Construction and modification of full-length TCR coding sequences for receptor design and engineering studies.
• Functional validation: Production of sequences for synthesis and transduction into cell lines (e.g., Jurkat) to assess antigen specificity.
• Large-scale repertoire generation: Generation of large TCR sequence sets for high-throughput repertoire analyses.
• Translational immunology: Facilitation of precise TCR construct production for basic and translational studies aimed at therapeutic development.

Methodology:

Assembles full-length coding nucleotide sequences by combining V and J gene-derived germline or user-supplied variable/constant sequences with CDR3 amino acid sequences to produce fully spliced TCR cDNA, with the Thimble script used for batch high-throughput processing.