Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes
René L. Warren,J. Douglas Freeman,Thomas Zeng,Gina Choe,Sarah A. Munro,Richard D. Moore,John R. Webb,Robert A. Holt +7 more
TLDR
It is shown that the sensitivity of sequence-based repertoire profiling is limited by both sequencing depth and sequencing accuracy, and a new, directly measured, lower limit on individual T-cell repertoire size is established.Abstract:
Massively parallel sequencing is a useful approach for characterizing T-cell receptor diversity. However, immune receptors are extraordinarily difficult sequencing targets because any given receptor variant may be present in very low abundance and may differ legitimately by only a single nucleotide. We show that the sensitivity of sequence-based repertoire profiling is limited by both sequencing depth and sequencing accuracy. At two timepoints, 1 wk apart, we isolated bulk PBMC plus naive (CD45RA+/CD45RO-) and memory (CD45RA-/CD45RO+) T-cell subsets from a healthy donor. From T-cell receptor beta chain (TCRB) mRNA we constructed and sequenced multiple libraries to obtain a total of 1.7 billion paired sequence reads. The sequencing error rate was determined empirically and used to inform a high stringency data filtering procedure. The error filtered data yielded 1,061,522 distinct TCRB nucleotide sequences from this subject which establishes a new, directly measured, lower limit on individual T-cell repertoire size and provides a useful reference set of sequences for repertoire analysis. TCRB nucleotide sequences obtained from two additional donors were compared to those from the first donor and revealed limited sharing (up to 1.1%) of nucleotide sequences among donors, but substantially higher sharing (up to 14.2%) of inferred amino acid sequences. For each donor, shared amino acid sequences were encoded by a much larger diversity of nucleotide sequences than were unshared amino acid sequences. We also observed a highly statistically significant association between numbers of shared sequences and shared HLA class I alleles.read more
Citations
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Characterization of Distinct T Cell Receptor Repertoires in Tumor and Distant Non-tumor Tissues from Lung Cancer Patients.
TL;DR: A comprehensive comparison of the TCR repertoires between cancer tissues and matched normal lung tissues is provided and the presence of distinct T cell immune microenvironments in lung cancer patients is demonstrated.
Journal ArticleDOI
Applications of systems biology in cancer immunotherapy: from target discovery to biomarkers of clinical outcome
TL;DR: In this article, the authors illustrate the contributions of systems biology towards the development and mechanistic understanding of cancer immunotherapies through some recently reported studies, such as DNA and protein microarrays, deep sequencing, mass spectrometry, as well as the computational methods for their analyses.
Journal ArticleDOI
Temporal Expression of Bim Limits the Development of Agonist-Selected Thymocytes and Skews Their TCRβ Repertoire
Kun-Po Li,Kun-Po Li,Anke Fähnrich,Eron Roy,Eron Roy,Carla M. Cuda,H. Leighton Grimes,H. Leighton Grimes,Harris Perlman,Kathrin Kalies,David A. Hildeman,David A. Hildeman +11 more
TL;DR: It is found that T cell–specific expression of Bim during early/cortical, but not late/medullary, thymic development controls the agonist selection of CD8αα precursors and their TCRβ repertoire and limits their private TCR β repertoire.
Journal ArticleDOI
Describing the diversity of Ag specific receptors in vertebrates: Contribution of repertoire deep sequencing.
Rosario Castro,Sofie Navelsaker,Sofie Navelsaker,Aleksei Krasnov,Louis Du Pasquier,Pierre Boudinot +5 more
TL;DR: This review provides a short overview of the technologies currently used to produce global description of immune repertoires, describe how they have already been used in comparative immunology, and discusses the future potential of such approaches.
Journal ArticleDOI
Tools for fundamental analysis functions of TCR repertoires: a systematic comparison.
Yanfang Zhang,Xiujia Yang,Yanxia Zhang,Yan Zhang,Minhui Wang,Jin Xia Ou,Yan Zhu,Huikun Zeng,Jiaqi Wu,Chunhong Lan,Hongwei Zhou,Wei Yang,Zhenhai Zhang +12 more
TL;DR: A systematic analysis of 12 available TCR repertoire analysis tools using simulated data, with an emphasis on fundamental analysis functions, sheds light on the detailed functions of TCR functionality analysis tools and may help researchers in the field to choose the right tools for their particular experimental design.
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