During early stages of the cell maturation process, a set of V (variable), D (diversity) and J (joining) gene segments are chosen from a genetically encoded pool to create a typically unique receptor for each B and T cell, a process known as V(D)J recombination. The B and T cells of the immune system of higher organisms create and express a vast array of different immunoglobulin (Ig) and T cell receptor (TCR) sequences, respectively, in order to target invading pathogens.
Immune repertoire capture standfod download#
The RDI method has been implemented as an R package, and is available for download through Bitbucket. We prove that the RDI method is an accurate and versatile method for comparisons of immune repertoires. We use the RDI method to recapitulate known differences in the formation of the CD4 + and CD8 + T cell repertoires, and further show that antigen-driven activation of naïve CD8 + T cells is more selective than in the CD4 + repertoire, resulting in a more specialized CD8 + memory repertoire. This method, referred to as the Repertoire Dissimilarity Index (RDI), uses a bootstrapped subsampling approach to account for variance in sequencing depth, and, coupled with a data simulation approach, allows for direct quantification of the average variation between repertoires. In this paper, we present a non-parametric method for directly comparing sequencing repertoires, with the goal of rigorously quantifying differences in V, D, and J gene segment utilization. However, methods for studying these repertoires, and for directly comparing different immune repertoires, are lacking. The sequencing and analysis of immune repertoires is emerging as an important tool to understand immune responses, whether beneficial or harmful (in the case of autoimmunity). The B and T cells of the human adaptive immune system leverage a highly diverse repertoire of antigen-specific receptors to protect the human body from pathogens.
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