Besides, most tools lack specific solutions to some common problems like systemic statistics and visualizations, PCR and sequencing errors, and amplification bias correction. Decombinator and MiTCR can only be used to analyze the TCR sequences. For instance, HighV-QEUST can be adopted to analyze both TCRs and BCRs, but its online version limits maximum sequence input to 150,000 at a time for regular users. These tools are equipped with useful functions, including V(D)J gene alignment, CDR3 sequence identification, and more, yet with obvious limitations.
#Tcr repertoire imgt software
Several tools and software have been developed for TCR and BCR sequence analysis, including iHMMune-align ( Gaeta 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. Recently, deep sequencing enabled by different platforms including Roche 454 and Illumina Hiseq ( Freeman et al. The T- and B-cell repertoire could undergo dynamic changes under different phenotypic status. In humans, it has been estimated theoretically that the diversity of TCR-αβ 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. 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). Structurally, each chain can be divided into the variable domain and the constant domain ( Lefranc and Lefranc 2001a, b). The TCR consists of a heterodimeric αβ chain (∼95%, TRA, TRB) or γδ chain (∼5%), while the BCR is assembled with two heavy chains (IGH) and two light chains (IGK or IGL). THE 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. In summary, this package would be of widespread usage for immune repertoire analysis. In the final part of this article, we demonstrate its application on minimal residual disease detection in patients with B-cell acute lymphoblastic leukemia. IMonitor provides general adaptation for sequences from all receptor chains of different species and outputs useful statistics and visualizations. 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. We compare IMonitor with other published tools by simulated and public rearranged sequences, and it demonstrates its superior performance in most aspects. This method utilizes realignment to identify V(D)J genes and alleles after common local alignment. We have developed a high-resolution analytical pipeline, Immune Monitor (“IMonitor”) to tackle this task. However, an efficient and accurate analytical tool is still on demand to process the huge amount of data. 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).
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