Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine

Thomas, Niclas; Heather, James; Ndifon, Wilfred; Shawe‐Taylor, John; Chain, Benjamin M.

doi:10.1093/bioinformatics/btt004

Cited by 96 publications

(92 citation statements)

References 23 publications

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“…Differences between thymic and blood TCR sequence distributions allow us to infer subtle details of this "turning on" of the mouse immune system. by distinct recombination events, standard tools that assign a unique recombination scenario to each sequence (17)(18)(19)(20) give biased estimates that would limit our ability to detect the developmental changes that interest us here. In previous work (9, 10) we showed how to overcome this problem, using an approach that assigns probabilities to different ways of generating a sequence (see Materials and Methods for details).…”

Section: Significancementioning

confidence: 99%

Insights into immune system development and function from mouse T-cell repertoires

Sethna

Elhanati

Dudgeon

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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The ability of the adaptive immune system to respond to arbitrary pathogens stems from the broad diversity of immune cell surface receptors. This diversity originates in a stochastic DNA editing process (VDJ recombination) that acts on the surface receptor gene each time a new immune cell is created from a stem cell. By analyzing T-cell receptor (TCR) sequence repertoires taken from the blood and thymus of mice of different ages, we quantify the changes in the VDJ recombination process that occur from embryo to young adult. We find a rapid increase with age in the number of random insertions and a dramatic increase in diversity. Because the blood accumulates thymic output over time, blood repertoires are mixtures of different statistical recombination processes, and we unravel the mixture statistics to obtain a picture of the time evolution of the early immune system. Sequence repertoire analysis also allows us to detect the statistical impact of selection on the output of the VDJ recombination process. The effects we find are nearly identical between thymus and blood, suggesting that our analysis mainly detects selection for proper folding of the TCR receptor protein. We further find that selection is weaker in laboratory mice than in humans and it does not affect the diversity of the repertoire.

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Section: Significancementioning

confidence: 99%

Insights into immune system development and function from mouse T-cell repertoires

Sethna

Elhanati

Dudgeon

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…Biases were assumed as independent for this model. In Simulation B, biases were measured from the raw data, processed by Decombinator (Thomas et al 2013). The following generation parameters were learned from the nonfunctional (out of frame) CDR3 sequences: V and J genes usage, conditional probabilities for deletions in each gene, and junctional nucleotide probabilities, including junction length.…”

Section: Library Preparation For Tcr-seq and Data Preprocessingmentioning

confidence: 99%

T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity

et al. 2014

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The T-cell receptor (TCR) repertoire is formed by random recombinations of genomic precursor elements; the resulting combinatorial diversity renders unlikely extensive TCR sharing between individuals. Here, we studied CDR3b amino acid sequence sharing in a repertoire-wide manner, using high-throughput TCR-seq in 28 healthy mice. We uncovered hundreds of public sequences shared by most mice. Public CDR3 sequences, relative to private sequences, are two orders of magnitude more abundant on average, express restricted V/J segments, and feature high convergent nucleic acid recombination. Functionally, public sequences are enriched for MHC-diverse CDR3 sequences that were previously associated with autoimmune, allograft, and tumor-related reactions, but not with anti-pathogen-related reactions. Public CDR3 sequences are shared between mice of different MHC haplotypes, but are associated with different, MHC-dependent, V genes. Thus, despite their random generation process, TCR repertoires express a degree of uniformity in their post-genomic organization. These results, together with numerical simulations of TCR genomic rearrangements, suggest that biases and convergence in TCR recombination combine with ongoing selection to generate a restricted subset of self-associated, public CDR3 TCR sequences, and invite reexamination of the basic mechanisms of T-cell repertoire formation. [Supplemental material is available for this article.]The genome provides the raw material for the somatic generation of enormous T-cell receptor (TCR) diversity. These receptors are generated through a random process of DNA rearrangement, which involves the recombination of the germline V, D, and J gene segments and the deletion and insertion of nucleotides at the V(D)J junctions. The variety of the resulting TCR repertoire is required to recognize a large and unpredictable range of antigens of foreign and self origin. The potential diversity of TCR molecules synthesized during the maturation of T cells in the thymus is estimated to be >10 15 for the mouse TCRA and TCRB repertoire (Casrouge et al. 2000) and >10 10 for the b segment of the TCR. In

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“…The TRA/TRB data were analyzed by HighV-QEUST (Li et al 2013), Decombinator (Thomas et al 2013), IgBLAST (Ye et al 2013), and IMonitor, while the IGH/IGK/ IGL data were analyzed by HighV-QEUST, IgBLAST (Ye et al 2013), and IMonitor. Thomas et al (2013) reported that The data sets were obtained from the IMGT/LIGM-DB database (http://www.imgt.org/ligmdb/); searched by "Homo sapiens," "rearranged," "TRB," or "IGH"; and then the selected sequences were annotated manually (Annot. level=="manual") and annotated by V, D, J genes.…”

Section: Imonitor Outperforms Other Analytical Tools In Various Aspectsmentioning

confidence: 99%

“…Several tools and software have been developed for TCR and BCR sequence analysis, including iHMMune-align (Gaeta et al 2007), HighV-QEUST (Li et al 2013), IgBLAST (Ye et al 2013), Decombinator (Thomas et al 2013), and MiTCR (Bolotin et al 2013). These tools are equipped with useful functions, including V(D)J gene alignment, CDR3 sequence identification, and more, yet with obvious limitations.…”

mentioning

confidence: 99%

IMonitor: A Robust Pipeline for TCR and BCR Repertoire Analysis

et al. 2015

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The advance of next generation sequencing (NGS) techniques provides an unprecedented opportunity to probe the enormous diversity of the immune repertoire by deep sequencing T-cell receptors (TCRs) and B-cell receptors (BCRs). However, an efficient and accurate analytical tool is still on demand to process the huge amount of data. We have developed a high-resolution analytical pipeline, Immune Monitor ("IMonitor") to tackle this task. This method utilizes realignment to identify V(D)J genes and alleles after common local alignment. We compare IMonitor with other published tools by simulated and public rearranged sequences, and it demonstrates its superior performance in most aspects. Together with this, a methodology is developed to correct the PCR and sequencing errors and to minimize the PCR bias among various rearranged sequences with different V and J gene families. IMonitor provides general adaptation for sequences from all receptor chains of different species and outputs useful statistics and visualizations. In the final part of this article, we demonstrate its application on minimal residual disease detection in patients with B-cell acute lymphoblastic leukemia. In summary, this package would be of widespread usage for immune repertoire analysis.KEYWORDS next generation sequencing; bioinformatics; immune repertoire; TCR/BCR T HE diversity of T-cell receptors (TCRs), B-cell receptors (BCRs), and secreting form antibodies makes up the core of the complicated immune system and serves as pivotal defensive components to protect the body against invading virus, bacteria, and other pathogens. The TCR consists of a heterodimeric ab chain (95%, TRA, TRB) or gd chain (5%), while the BCR is assembled with two heavy chains (IGH) and two light chains (IGK or IGL). Structurally, each chain can be divided into the variable domain and the constant domain (Lefranc and Lefranc 2001a,b). The diversity of the TCR and BCR repertoire is enormous, owing to the process of V(D)J gene rearrangement, random deletion of germline nucleotides, and insertion of uncertain length of nontemplate nucleotides between V-D and D-J junctions (TRB, IGH) or V-J junctions (TRA, IGK, IGL). In humans, it has been estimated theoretically that the diversity of TCR-ab receptors exceeds 10 18 in the thymus, and the diversity of the B-cell repertoire is even larger, considering the somatic hypermutation (Janeway 2005;Benichou et al. 2012). The T-and B-cell repertoire could undergo dynamic changes under different phenotypic status. Recently, deep sequencing enabled by different platforms including Roche 454 and Illumina Hiseq (Freeman et al. 2009;Robins et al. 2009;Wang et al. 2010;Fischer 2011;Venturi et al. 2011) has been applied to unravel the dynamics of the TCR and BCR repertoire and extended to various translational applications such as vaccination, cancer, and autoimmune diseases.Several tools and software have been developed for TCR and BCR sequence analysis, including iHMMune-align (Gaeta et al. 2007), HighV-QEUST (Li et al. 2013), IgBLA...

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Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine

Abstract: The Decombinator package is implemented in Python (v2.6) and is freely available at https://github.com/uclinfectionimmunity/Decombinator along with full documentation and examples of typical usage.

Cited by 96 publications

References 23 publications

Insights into immune system development and function from mouse T-cell repertoires

Insights into immune system development and function from mouse T-cell repertoires

T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity

IMonitor: A Robust Pipeline for TCR and BCR Repertoire Analysis

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