Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq. Issue 1 (December 2016)

• Record Type: Journal Article
• Authors: Redmond, David; Poran, Asaf; Elemento, Olivier
• Is Part Of: Genome medicine. Volume 8:Issue 1(2016)
• Page Start: 1
• Page End: 12
• Publication Date: 2016-12
• Subjects: Genomics -- Periodicals; Medical genetics -- Periodicals; 616.042
• DOI: 10.1186/s13073-016-0335-7
• Languages: English
• ISSNs: 1756-994X

Abstract

Abstract 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 athttps://github.com/ElementoLab/scTCRseq .