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
IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling
Shuo Li,Marie-Paule Lefranc,John J. Miles,John J. Miles,John J. Miles,Eltaf Alamyar,Véronique Giudicelli,Patrice Duroux,J. Douglas Freeman,Vincent Corbin,Vincent Corbin,Jean-Pierre Y. Scheerlinck,Michael A. Frohman,Paul U. Cameron,Magdalena Plebanski,Bruce E. Loveland,Bruce E. Loveland,Scott R. Burrows,Anthony T. Papenfuss,Anthony T. Papenfuss,Eric J. Gowans,Eric J. Gowans +21 more
TL;DR: A next generation methodology, which combines 5′RACE PCR, 454 sequencing and IMGT, is described, which achieves a degree of resolution for next generation sequencing verifiable by the user at the sequence level, while providing a normalized reference immunoprofile for human TRB.
Journal ArticleDOI
Ultra-sensitive detection of rare T cell clones
Harlan Robins,Cindy Desmarais,Jessica Matthis,Robert J. Livingston,Jessica Andriesen,Helena Reijonen,Christopher S. Carlson,Gerold Nepom,Cassian Yee,Karen Cerosaletti +9 more
TL;DR: A multiplex PCR method to sequence tens of millions of T cell receptors (TCRs) from a single sample in a few days is developed, able to detect even the rarest clones.
Journal ArticleDOI
Quantitative assessment of T cell repertoire recovery after hematopoietic stem cell transplantation
Jeroen W. J. van Heijst,Izaskun Ceberio,Lauren Lipuma,Dane W Samilo,Gloria Wasilewski,Anne Marie Gonzales,Jimmy Nieves,Marcel R.M. van den Brink,Marcel R.M. van den Brink,Miguel Perales,Miguel Perales,Eric G. Pamer +11 more
TL;DR: The combined use of 5′ rapid amplification of complementary DNA ends PCR with deep sequencing to quantify TCR diversity in 28 recipients of allo-HSCT using a single oligonucleotide pair provides unprecedented views of T cell repertoire recovery after allo -HSCT and may identify patients at high risk of infection or relapse.
Journal ArticleDOI
Next generation sequencing for tcr repertoire profiling: platform-specific features and correction algorithms
Dmitry A. Bolotin,Ilgar Z. Mamedov,Olga V. Britanova,Ivan V. Zvyagin,Dmitriy A. Shagin,Svetlana V. Ustyugova,Maria A. Turchaninova,Sergey Lukyanov,Yury B. Lebedev,Dmitriy M. Chudakov +9 more
TL;DR: It is demonstrated that advanced correction allows the removal of the majority of artificial TCR diversity with concomitant rescue of most of the sequencing information, and this correction enhances the accuracy of clonotype identification and quantification as well as overall TCR Diversity measurements.
Journal ArticleDOI
High-resolution antibody dynamics of vaccine-induced immune responses
Uri Laserson,Uri Laserson,Francois Vigneault,Daniel Gadala-Maria,Gur Yaari,Mohamed Uduman,Jason A. Vander Heiden,William Kelton,Sang Taek Jung,Yi Liu,Jonathan Laserson,Raj Chari,Je-Hyuk Lee,Ido Bachelet,Brendan Hickey,Erez Lieberman-Aiden,Bozena Hanczaruk,Birgitte B. Simen,Michael Egholm,Daphne Koller,George Georgiou,Steven H. Kleinstein,George M. Church +22 more
TL;DR: This work describes a set of tools for the analysis of antibody repertoires and their application to elucidating the dynamics of the response to viral vaccination in human volunteers and demonstrates one of the first characterizations of the fast antibody dynamics through time in multiple individuals responding to an immune challenge.
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.