Profiling genes encoding the adaptive immune receptor repertoire with gAIRR Suite.
Profiling genes encoding the adaptive immune receptor repertoire with gAIRR Suite.
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DOI：
10.3389/fimmu.2022.922513
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发表时间：
2022
影响因子：
7.3
通讯作者：
中科院分区：
文献类型：
--
作者：
适应性免疫受体库（AIRR）由T细胞受体（TR）和免疫球蛋白（IG）基因编码。分析这些编码AIRR（缩写为gAIRR）的生殖系基因对于理解适应性免疫应答是重要的，但由于高度遗传复杂性而具有挑战性。我们的gAIRR套件包括三个模块。gAIRR-seq是一种基于探针捕获的靶向测序管道，可对单个DNA样本的gAIRR进行分析。gAIRR-调用和gAIRR-注释调用等位基因分别来自gAIRR-seq读数和注释全基因组组装。我们以100%的准确率对7个瓶内基因组（GIAB）DNA样品的TRV和TRJ进行了gAIRR测序，并发现了新的等位基因。我们还从外周血单个核细胞（PBMC）和口腔粘膜细胞中gAIRR-测序和gAIRR-调用TR和IG基因。来自这两种细胞类型的调用结果具有高一致性（对于所有已知的gAIRR等位基因为99%）。我们gAIRR注释了36个基因组，发现了325个新的TRV等位基因和29个新的TRJ等位基因。我们可以进一步分析侧翼序列，包括重组信号序列（RSS）。我们验证了HG 002的两种结构变体，并发现了参考文献GRCh 37和GRCh 38中gAIRR基因的实质性差异。gAIRR Suite可作为测序、分析和验证生殖系TR和IG基因的资源，以研究各种免疫相关表型。
Adaptive immune receptor repertoire (AIRR) is encoded by T cell receptor (TR) and immunoglobulin (IG) genes. Profiling these germline genes encoding AIRR (abbreviated as gAIRR) is important in understanding adaptive immune responses but is challenging due to the high genetic complexity. Our gAIRR Suite comprises three modules. gAIRR-seq, a probe capture-based targeted sequencing pipeline, profiles gAIRR from individual DNA samples. gAIRR-call and gAIRR-annotate call alleles from gAIRR-seq reads and annotate whole-genome assemblies, respectively. We gAIRR-seqed TRV and TRJ of seven Genome in a Bottle (GIAB) DNA samples with 100% accuracy and discovered novel alleles. We also gAIRR-seqed and gAIRR-called the TR and IG genes of a subject from both the peripheral blood mononuclear cells (PBMC) and oral mucosal cells. The calling results from these two cell types have a high concordance (99% for all known gAIRR alleles). We gAIRR-annotated 36 genomes to unearth 325 novel TRV alleles and 29 novel TRJ alleles. We could further profile the flanking sequences, including the recombination signal sequence (RSS). We validated two structural variants for HG002 and uncovered substantial differences of gAIRR genes in references GRCh37 and GRCh38. gAIRR Suite serves as a resource to sequence, analyze, and validate germline TR and IG genes to study various immune-related phenotypes.
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影响因子：
56.9
作者：
Arstila, TP;Casrouge, A;Kourilsky, P
通讯作者：
Kourilsky, P
影响因子：
56.9
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通讯作者：
Phillippy, Adam M
影响因子：
17.1
作者：
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DOI：
10.1073/pnas.1417683112
发表时间：
2015-02-24
影响因子：
11.1
作者：
Gadala-Maria, Daniel;Yaari, Gur;Kleinstein, Steven H.
通讯作者：
Kleinstein, Steven H.