The Decombinator is a toolkit for analyzing TCR from short reads ( 22). It is based on pyromap that is specifically designed for 454 pyrosequencing platform ( 21) thus, it does not fit with other sequencing platforms. In contrast, the IRmap is a program that maps the sequencing reads to reference V and J gene segments ( 5).
Tcr repertoire imgt software#
However, the program can only analyze the assembled paired-end reads, and no software was released to the public. The algorithm is based on sequencing reads alignment with reference V gene and J gene segments for the identification of TCR sequences, as well as applying a 96% cutoff value on J gene segment diversity. More recently, the iSSAKE-like strategy was developed by Warren et al. Because of the sequencing cost, short paired-end reads generated by next-generation sequencing technology are and will remain the main source of data, and we believe that the TCRklass is a useful and reliable toolkit for TCR repertoire analysis. We applied TCRklass on large datasets of two human and three mouse TCR repertoires it demonstrated higher reliability on CDR3 identification and much less biased V/J profiling, which are the two components contributing the diversity of the repertoire.
We tested TCRklass using manually curated short read datasets in comparison with in silico datasets it showed higher precision and recall rates on CDR3 identification. To decipher the complexity of TCR repertoire, we developed an integrated pipeline, TCRklass, using K-string–based algorithm that has significantly improved the accuracy and performance over existing tools. Am J Clin Pathol 121:373–383ĭziubianau M, Hecht J, Kuchenbecker L, Sattler A, Stervbo U, Rödelsperger C et al (2013) TCR repertoire analysis by next generation sequencing allows complex differential diagnosis of T cell–related pathology.The next-generation sequencing technology has promoted the study on human TCR repertoire, which is essential for the adaptive immunity. Morice WG, Kimlinger T, Katzmann JA, Lust JA, Heimgartner PJ, Halling KC et al (2004) Flow cytometric assessment of TCR-Vβ expression in the evaluation of peripheral blood involvement by T-cell lymphoproliferative disorders a comparison with conventional T-cell immunophenotyping and molecular genetic techniques. Van der Geest KSM, Abdulahad WH, Horst G, Lorencetti PG, Bijzet J, Arends S et al (2015) Quantifying distribution of flow cytometric TCR-Vβ usage with economic statistics. Lefranc MPM (2003) IMGT the internationaal ImMunoGeneTics database. Wei S, Charmley P, Robinson MA, Concannon P (1994) The extent of the human germline T-cell receptor V beta gene segment repertoire. Langerak AW, van den Beemd R, Wolvers-Tetter ILM, Boor PPC, van Lochem EG, Hooijkaas H et al (2001) Molecular and flow cytometric analysis of the Vb repertoire for clonality assessment in mature TCRab T-cell proliferations. Tembhare P, Yuan CM, Xi L, Morris JC, Liewehr D, Venzon D et al (2001) Flow cytometric immunophenotypic assessment of T-cell clonality by Vβ repertoire analysis detection of T-cell Clonality at diagnosis and monitoring of minimal residual disease following therapy. Van den Beemd R, Boor PPC, van Lochem EG, Hop WCJ, Langerak AW, Wolvers-Tetter ILM et al (2000) Flow cytometric analysis of the Vb repertoire in healthy controls. Davis MM, Bjorkman PJ (1988) T-cell antigen receptor genes and T-cell recognition.
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