Targeted long-read sequencing facilitates phased diploid assembly and genotyping of the human T cell receptor alpha, delta, and beta loci.
Targeted long-read sequencing facilitates phased diploid assembly and genotyping of the human T cell receptor alpha, delta, and beta loci.
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DOI：
10.1016/j.xgen.2022.100228
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发表时间：
2022-12-14
期刊：
影响因子：
--
通讯作者：
Watson, Corey T.
中科院分区：
文献类型：
--
作者：
Rodriguez, Oscar L.;Silver, Catherine A.;Shields, Kaitlyn;Smith, Melissa L.;Watson, Corey T.
T细胞受体（TCR）识别由主要组织相容性复合体（MHC）呈递的肽片段，并且对T细胞介导的免疫至关重要。最近的数据表明，TCR编码基因区域内的遗传多样性研究不足，限制了对疾病中TCR基因座多态性对TCR功能的影响的理解，即使TCR库签名（1）是可遗传的，（2）与疾病表型相关。为了解决这一问题，我们开发了一种靶向长读段测序方法，以生成TCR β（TRB）和α/δ（TRA/D）基因座的高度准确的单倍型分辨组装，促进所有变体类型（包括结构变体）的基因分型。我们使用两个母亲-父亲-孩子三人组和5个代表多个人群的无关供体来验证我们的方法。这提高了基因分型的准确性，并发现了84个未记录的V、D、J和C等位基因，证明了该框架对于提高我们对疾病中TCR多样性和功能的理解的实用性。用于表征T细胞受体基因座中基因组多样性的新框架基准测试揭示了准确的组装，变异调用，和基因注释集使用长读序测序框架的变体检测优于短读序方法发现大量先前未记录的T细胞受体基因等位基因T细胞受体（TCR）基因内的遗传变异影响TCR库和TCR-肽的组成。主要组织相容性复合体相互作用然而，人类TCR基因座内的多样性没有很好的记录。Rodriguez等人报道了一种新的可扩展的方法，用于TCR β、α和δ基因座的靶向长读序测序。
T cell receptors (TCRs) recognize peptide fragments presented by the major histocompatibility complex (MHC) and are critical to T cell-mediated immunity. Recent data have indicated that genetic diversity within TCR-encoding gene regions is underexplored, limiting understanding of the impact of TCR loci polymorphisms on TCR function in disease, even though TCR repertoire signatures (1) are heritable and (2) associate with disease phenotypes. To address this, we developed a targeted long-read sequencing approach to generate highly accurate haplotype resolved assemblies of the TCR beta (TRB) and alpha/delta (TRA/D) loci, facilitating the genotyping of all variant types, including structural variants. We validate our approach using two mother-father-child trios and 5 unrelated donors representing multiple populations. This resulted in improved genotyping accuracy and the discovery of 84 undocumented V, D, J, and C alleles, demonstrating the utility of this framework for improving our understanding of TCR diversity and function in disease. Novel framework to characterize genomic diversity in the T cell receptor loci Benchmarking revealed accurate assemblies, variant calls, and gene annotation sets Variant detection with long-read sequencing framework outperforms short-read methods Discovery of large number of previously undocumented T cell receptor gene alleles Genetic variation within T cell receptor (TCR) genes influences the composition of the TCR repertoire and TCR-peptide-major histocompatibility complex interactions. Yet, diversity within human TCR loci is not well documented. Rodriguez et al. report a novel scalable method for targeted long-read sequencing of the TCR beta, alpha, and delta loci.
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