Single cell TCRseq: paired recovery of entire T cell alpha and beta chain transcripts in T cell receptors from single cell RNAseq
Accurate characterization of the repertoire of the T cell receptor (TCR) alpha and beta chains is critical to understanding adaptive immunity. Such characterization has many applications across such fields as vaccine development and response, clone tracking in cancer, and immunotherapy. Here we present a new methodology called single cell TCRseq (scTCRseq) for the identification and assembly of full length rearranged V(D)J T cell receptor sequences from paired end single cell RNA sequencing reads. The method allows accurate identification of the V(D)J rearrangements for each individual T cell and has the novel ability to recover paired alpha and beta segments. Source code is available at https:/github.com/ElementoLab/scTCRseq.
Genome Medicine