The TCR repertoire can provide insights into immunodominance, functionality, and the protective effects of the T cell response (16, 17). Finally, we present an overview of the available software tools that can be used to perform integrative analysis of gene expression and TCR profiles. Thereafter we performed T cell receptor (TCR) repertoire analysis of various specimens in clinical settings including cytomegalovirus (CMV), polyomavi- rus BK (. TCR repertoire analysis is also proving useful as a biomarker of the response to immunotherapy. In addition, this review provides detailed descriptions of recent computational developments for analyzing single-cell TCR sequencing data in an integrative manner using novel computational approaches. Here we discuss the current progress in the field of single-cell T cell sequencing, with a focus on the multimodality of new approaches that allow the paired profiling of cellular phenotype and clonotype information. Consequently, this prompts the need for the development of novel computational tools that integrate transcriptomic profiles and corresponding features of the TCR repertoire. Recently, single-cell technologies have gained in popularity due to improvements in throughput, decrease in cost and the ability for multimodal experiments that integrate different information layers. Moreover, the associations between TCR repertoire metrics and tumor mutation burden (TMB), as well as programmed death-ligand 1 were explored, respectively. This combination of transcriptomic- and repertoire information can provide novel insight into the functional character of T cell immunity. The TCR repertoire is dynamic, as lymphocytes are continuously generated, die and expand in response to stimulation, and reflects both an individual’s immune potential and history. Comprehensive analysis of TCR repertoire metrics was performed with different KRAS mutation subtypes and concomitant mutations. Here we present UcTCRdb, a database that contains 669,900 unconventional TCRs collected from 34 corresponding studies in humans, mice, and cattle. In contrast, conventional bulk methods are restricted to only one layer of information. The small size and irregularities of the released unconventional TCR sequences are far from high-quality to support systemic analysis of unconventional TCR repertoire. Single-cell sequencing technologies have paved the road for interrogating the transcriptome and the paired αβ TCR repertoire of a single T cell in tandem. Through the unique mechanism of V(D)J recombination, T cells express a highly specific receptor complex known as the T-cell receptor (TCR). T cells exercise a multitude of functions such as cytotoxicity, secretion of immunomodulating cytokines or regulation of tolerance, collectively resulting in an effective control of immune-related disease.
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