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
Journal ArticleDOI
The Course of Immune Stimulation by Photodynamic Therapy: Bridging Fundamentals of Photochemically Induced Immunogenic Cell Death to the Enrichment of T-Cell Repertoire.
TL;DR: A hypothesis is postulate that during the course of the immune stimulation process, PDT also enriches the T‐cell repertoire with tumor‐reactive activated T cells, diversifying their tumor‐specific targets and eliciting a more expansive and rigorous antitumor response.
Journal ArticleDOI
Profiling tissue-resident T cell repertoires by RNA sequencing.
TL;DR: This method circumvents the need for PCR amplification of the TCR template and provides TCR information in the context of global gene expression, allowing integrated analysis of extensive RNA-sequencing data resources.
Journal ArticleDOI
Quantitative Profiling of Immune Repertoires for Minor Lymphocyte Counts Using Unique Molecular Identifiers
Evgeny S. Egorov,Ekaterina M. Merzlyak,Andrew A. Shelenkov,Olga V. Britanova,George V. Sharonov,George V. Sharonov,Dmitriy B. Staroverov,Dmitriy A. Bolotin,Alexey N. Davydov,Ekaterina V. Barsova,Y B Lebedev,Mikhail Shugay,Mikhail Shugay,Mikhail Shugay,Dmitriy M. Chudakov,Dmitriy M. Chudakov,Dmitriy M. Chudakov +16 more
TL;DR: A robust approach based on unique molecular identifiers that allows profiling Ag receptors for several hundred to thousand lymphocytes while preserving qualitative and quantitative information on clonal composition of the sample is reported.
Journal ArticleDOI
Peripheral selection rather than thymic involution explains sudden contraction in naive CD4 T-cell diversity with age
TL;DR: This work proposes that an abrupt decline in the repertoire could be caused by the accumulation of mutations that provide a short-term fitness advantage to a small number of T-cell clones, with the person as a whole incurring the long-term cost of a decreased ability to fight infections.
Journal ArticleDOI
A high density of tertiary lymphoid structure B cells in lung tumors is associated with increased CD4(+) T cell receptor repertoire clonality.
Wei Zhu,Claire Germain,Zheng Liu,Yinong Sebastian,Priyanka Devi,Samantha Knockaert,Philip Brohawn,Kim Lehmann,Diane Damotte,Pierre Validire,Yihong Yao,Viia Valge-Archer,Scott A. Hammond,Marie-Caroline Dieu-Nosjean,Brandon W. Higgs +14 more
TL;DR: Results indicate distinct adaptive immune responses in NSCLC, where peripheral T cell diversity is modulated by age, and tumor T cell clonal expansion is favored by the presence of TLSs in the tumor microenvironment.
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.