title: Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq.
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 at https://github.com/ElementoLab/scTCRseq .
authors.affiliation: Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA.|Institute for Computational Biomedicine & Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.
authors.forename: David
authors.initials: D
authors.lastname: Redmond
authors.affiliation: Institute for Computational Biomedicine & Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.
authors.forename: Asaf
authors.initials: A
authors.lastname: Poran
authors.affiliation: Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA. ole2001@med.cornell.edu.|Institute for Computational Biomedicine & Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA. ole2001@med.cornell.edu.
authors.forename: Olivier
authors.initials: O
authors.lastname: Elemento
mesh_terms: D056704:Adaptive Immunity; D000818:Animals; D005786:Gene Expression Regulation; D015332:Gene Rearrangement, alpha-Chain T-Cell Antigen Receptor; D015333:Gene Rearrangement, beta-Chain T-Cell Antigen Receptor; D006801:Humans; D019169:Jurkat Cells; D051379:Mice; D012333:RNA, Messenger / Q000235:genetics* / Q000276:immunology; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000235:genetics* / Q000276:immunology; D017423:Sequence Analysis, RNA / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods*; D013601:T-Lymphocytes / Q000166:cytology / Q000276:immunology; D060152:V(D)J Recombination
chemical_list: D012333:RNA, Messenger; D016693:Receptors, Antigen, T-Cell, alpha-beta