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Genome Med. 2016 Jul 27;8(1):80. doi: 10.1186/s13073-016-0335-7.

Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq.

Author information

1
Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA.
2
Institute for Computational Biomedicine & Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.
3
Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA. ole2001@med.cornell.edu.
4
Institute for Computational Biomedicine & Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA. ole2001@med.cornell.edu.

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 .

PMID:
27460926
PMCID:
PMC4962388
DOI:
10.1186/s13073-016-0335-7
[Indexed for MEDLINE]
Free PMC Article

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