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
More filters
Patent
Determining antigen-specific t-cells
Mark Klinger,Faham Malek +1 more
TL;DR: In this paper, a method for determining antigen-specific T cells was proposed, which can be implemented by reacting under interaction conditions one or more antigens with T cells in a plurality of subsets of a tissue sample, such as peripheral blood, sorting antigen-interacting T cells from other T cells, and separately sequencing for each subset recombined nucleic acid encoding a segment of a TCR chain from a sample of T cells prior to exposure to antigen and from a sampled T cells isolated based on their interaction with antigen.
Journal ArticleDOI
The somatically generated portion of T cell receptor CDR3α contributes to the MHC allele specificity of the T cell receptor
Philippa Marrack,Philippa Marrack,Sai Harsha Krovi,Daniel Silberman,Janice White,Eleanor Kushnir,Maki Nakayama,James Crooks,Thomas Danhorn,Sonia M. Leach,Randy Anselment,James P. Scott-Browne,Laurent Gapin,John W. Kappler,John W. Kappler +14 more
TL;DR: It is shown that positive selection-induced MHC bias of T cell receptors is affected both by the germline encoded elements of the T cell receptor α and β chain and, surprisingly, dramatically affected by the non germ line encoded portions of CDR3 of the MHC receptor α chain.
Journal ArticleDOI
Shorter TCR β-Chains Are Highly Enriched During Thymic Selection and Antigen-Driven Selection
Xianliang Hou,Ping Zeng,Xujun Zhang,Jianing Chen,Yan Liang,Jiezuan Yang,Yida Yang,Xiangdong Liu,Hongyan Diao +8 more
TL;DR: It may be evolutionary pressures drive short CDR3s to recognize most of antigen in nature and be highly enriched during thymic selection and antigen-driven selection, and further enriched in public T-cell responses.
Journal ArticleDOI
Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition
Dina Schneidman-Duhovny,Natalia Khuri,Guang Qiang Dong,Michael B. Winter,Eric Shifrut,Nir Friedman,Charles S. Craik,Charles S. Craik,Kathleen P. Pratt,Pedro Paz,Fred Aswad,Andrej Sali +11 more
TL;DR: This work presents a method, ITCell, for prediction of T-cell epitopes within an input protein antigen sequence for given MHCII and TCR sequences that is more accurate than current single-stage epitope prediction algorithms applied to the same benchmarks.
Journal ArticleDOI
Dynamics of thymus function and T cell receptor repertoire breadth in health and disease.
TL;DR: In this article, the importance of thymic function for generation of the TCR repertoire and how acute and chronic damage influences immune health is discussed, as well as methods that are used to measure Thymic Function in patients.
References
More filters
Journal ArticleDOI
Clustal W and Clustal X version 2.0
Mark A. Larkin,Gordon Blackshields,Nigel P. Brown,R. Chenna,Paul A. McGettigan,Hamish McWilliam,Franck Valentin,Iain M. Wallace,Andreas Wilm,Rodrigo Lopez,J.D. Thompson,Toby J. Gibson,Desmond G. Higgins +12 more
TL;DR: The Clustal W and ClUSTal X multiple sequence alignment programs have been completely rewritten in C++ to facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.
Journal ArticleDOI
Base-calling of automated sequencer traces using Phred. I. accuracy assessment
TL;DR: In this article, a base-calling program for automated sequencer traces, phred, with improved accuracy was proposed. But it was not shown to achieve a lower error rate than the ABI software, averaging 40%-50% fewer errors in the data sets examined independent of position in read, machine running conditions, or sequencing chemistry.
Journal ArticleDOI
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Brent Ewing,Philip Green +1 more
TL;DR: The ability to estimate a probability of error for each base-call, as a function of certain parameters computed from the trace data, is developed and implemented in the base-calling program.
Journal ArticleDOI
T-cell antigen receptor genes and T-cell recognition.
Mark M. Davis,Pamela J. Bjorkman +1 more
TL;DR: This view of T-cell recognition has implications for how the receptors might be selected in the thymus and how they (and immunoglobulins) may have arisen during evolution.
Journal ArticleDOI
Nomenclature for factors of the HLA system, 2010.
Steven G.E. Marsh,E. D. Albert,Walter F. Bodmer,Ronald E. Bontrop,Bo Dupont,Henry A. Erlich,Marcelo Fernandez-Vina,Daniel E. Geraghty,Rhonda Holdsworth,Carolyn Katovich Hurley,M. Lau,Keun-Seok Lee,Bernard Mach,Martin Maiers,Wolfgang R. Mayr,Carlheinz Müller,Peter Parham,Effie W. Petersdorf,Takehiko Sasazuki,Jack L. Strominger,A. Svejgaard,Paul I. Terasaki,Jean-Marie Tiercy,John Trowsdale +23 more
TL;DR: This report documents the additions and revisions to the nomenclature of HLA specificities following the principles established in previous reports.