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

被引：0
作者：
David Redmond
Asaf Poran
Olivier Elemento
机构：
[1] Tri-Institutional Training Program in Computational Biology and Medicine,Institute for Computational Biomedicine & Institute for Precision Medicine
[2] Weill Cornell Medicine,undefined
来源：
Genome Medicine | / 8卷
关键词：
Read Length; Alpha Chain; Beta Chain; Jurkat Cell Line; TRBV Gene;
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摘要：
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.
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  • [1] Han A(2014)Linking T-cell receptor sequence to functional phenotype at the single-cell level Nat Biotechnol 32 684-92
  • [2] Glanville J(2014)An ID card for T cells Nat Biotechnol 32 639-40
  • [3] Hansmann L(2011)Paired analysis of TCRα and TCRβ chains at the single-cell level in mice J Clin Invest 121 288-95
  • [4] Davis MM(2013)High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire Nat Biotechnol 31 166-9
  • [5] Jiang N(2015)High-throughput pairing of T cell receptor and sequences Sci Transl Med 7 301ra131-ra301ra131
  • [6] Zhang S(2013)Preparing unbiased T-cell receptor and antibody cDNA libraries for the deep next generation sequencing profiling Front Immunol. 4 456-6
  • [7] Ma K(2014)Quantitative assessment of single-cell RNA-sequencing methods Nat Methods 11 41-40
  • [8] Dash P(2013)Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells Nature 498 236-68
  • [9] McClaren JL(2014)The promise and challenge of high-throughput sequencing of the antibody repertoire Nat Biotechnol 32 158-42
  • [10] Oguin TH(2015)Estimating T-cell repertoire diversity: limitations of classical estimators and a new approach Philos Trans R Soc Lond B Biol Sci 370 20140291-53
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