适应性免疫受体库 (AIRR) 社区对库分析的指南。
Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis.
机构信息
Department of Pathology, Yale School of Medicine, New Haven, CT, USA.
Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland.
出版信息
Methods Mol Biol. 2022;2453:297-316. doi: 10.1007/978-1-0716-2115-8_17.
Abstract
Adaptive immune receptor repertoires (AIRRs) are rich with information that can be mined for insights into the workings of the immune system. Gene usage, CDR3 properties, clonal lineage structure, and sequence diversity are all capable of revealing the dynamic immune response to perturbation by disease, vaccination, or other interventions. Here we focus on a conceptual introduction to the many aspects of repertoire analysis and orient the reader toward the uses and advantages of each. Along the way, we note some of the many software tools that have been developed for these investigations and link the ideas discussed to chapters on methods provided elsewhere in this volume.
摘要
适应性免疫受体库 (AIRR) 中蕴含着丰富的信息，可用于深入了解免疫系统的工作原理。基因使用、CDR3 特性、克隆谱系结构和序列多样性都能够揭示疾病、疫苗接种或其他干预措施对动态免疫反应的影响。在这里，我们重点介绍了对库分析的多个方面的概念性介绍，并引导读者了解每种方法的用途和优势。在这个过程中，我们注意到了许多为此类研究开发的软件工具，并将讨论的思路与本卷其他章节中提供的方法章节联系起来。
相似文献
1
Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis.适应性免疫受体库 (AIRR) 社区对库分析的指南。
Methods Mol Biol. 2022;2453:297-316. doi: 10.1007/978-1-0716-2115-8_17.
2
AIRR Community Guide to Planning and Performing AIRR-Seq Experiments.AIRR 社区 AIRR-Seq 实验规划和执行指南
Methods Mol Biol. 2022;2453:261-278. doi: 10.1007/978-1-0716-2115-8_15.
3
Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation.适应性免疫受体库（AIRR）TR 和 IG 基因注释社区指南。
Methods Mol Biol. 2022;2453:279-296. doi: 10.1007/978-1-0716-2115-8_16.
4
Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires.计算策略解析适应性免疫受体的高维复杂性。
Front Immunol. 2018 Feb 21;9:224. doi: 10.3389/fimmu.2018.00224. eCollection 2018.
5
The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories.CAIRR 管道用于向国家生物技术信息中心存储库提交符合标准的 B 和 T 细胞受体文库测序研究。
Front Immunol. 2018 Aug 16;9:1877. doi: 10.3389/fimmu.2018.01877. eCollection 2018.
6
sumrep: A Summary Statistic Framework for Immune Receptor Repertoire Comparison and Model Validation.sumrep：免疫受体库比较和模型验证的综合统计框架。
Front Immunol. 2019 Nov 1;10:2533. doi: 10.3389/fimmu.2019.02533. eCollection 2019.
7
AIRR Community Standardized Representations for Annotated Immune Repertoires.AIRR 社区注释免疫受体的标准化表示。
Front Immunol. 2018 Sep 28;9:2206. doi: 10.3389/fimmu.2018.02206. eCollection 2018.
8
Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification.分析机器学习模型在适应性免疫受体谱系分类中的基线性能和极限。
Gigascience. 2022 May 25;11. doi: 10.1093/gigascience/giac046.
9
Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling.用于适应性免疫受体谱分析的标准化和解释的生物学控制。
Elife. 2021 May 26;10:e66274. doi: 10.7554/eLife.66274.
10
OGRDB: a reference database of inferred immune receptor genes.OGRDB：一个推断的免疫受体基因参考数据库。
Nucleic Acids Res. 2020 Jan 8;48(D1):D964-D970. doi: 10.1093/nar/gkz822.
引用本文的文献
1
The BCR-SEQC initiative.BCR-SEQC计划。
Nat Immunol. 2025 Jul;26(7):978-979. doi: 10.1038/s41590-025-02196-6.
2
nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework.nf-core/airrflow：采用 Immcantation 框架的适应性免疫受体库分析工作流程。
PLoS Comput Biol. 2024 Jul 26;20(7):e1012265. doi: 10.1371/journal.pcbi.1012265. eCollection 2024 Jul.
3
Application and challenges of TCR and BCR sequencing to investigate T- and B-cell clonality in elastase-induced experimental murine abdominal aortic aneurysm.TCR和BCR测序在研究弹性蛋白酶诱导的实验性小鼠腹主动脉瘤中T细胞和B细胞克隆性方面的应用及挑战
Front Cardiovasc Med. 2023 Nov 14;10:1221620. doi: 10.3389/fcvm.2023.1221620. eCollection 2023.
4
Adaptive immune receptor genotyping using the program.采用 程序进行适应性免疫受体基因分型。
Front Immunol. 2023 Apr 11;14:1125884. doi: 10.3389/fimmu.2023.1125884. eCollection 2023.
本文引用的文献
1
Phylogenetic analysis of migration, differentiation, and class switching in B cells.B 细胞迁移、分化和类别转换的系统发生分析。
PLoS Comput Biol. 2022 Apr 25;18(4):e1009885. doi: 10.1371/journal.pcbi.1009885. eCollection 2022 Apr.
2
ClusTCR: a python interface for rapid clustering of large sets of CDR3 sequences with unknown antigen specificity.ClusTCR：一种用于快速聚类具有未知抗原特异性的大量 CDR3 序列的 Python 接口。
Bioinformatics. 2021 Dec 11;37(24):4865-4867. doi: 10.1093/bioinformatics/btab446.
3
Genetic Bias, Diversity Indices, Physiochemical Properties and CDR3 Motifs Divide Auto-Reactive from Allo-Reactive T-Cell Repertoires.遗传偏见、多样性指数、理化性质和 CDR3 基序将自身反应性和同种反应性 T 细胞库区分开来。
Int J Mol Sci. 2021 Feb 5;22(4):1625. doi: 10.3390/ijms22041625.
4
TCR/BCR dual-expressing cells and their associated public BCR clonotype are not enriched in type 1 diabetes.TCR/BCR 双表达细胞及其相关公共 BCR 克隆型在 1 型糖尿病中并不富集。
Cell. 2021 Feb 4;184(3):827-839.e14. doi: 10.1016/j.cell.2020.11.035.
5
The intratumoral CXCR3 chemokine system is predictive of chemotherapy response in human bladder cancer.肿瘤内 CXCR3 趋化因子系统可预测人类膀胱癌的化疗反应。
Sci Transl Med. 2021 Jan 13;13(576). doi: 10.1126/scitranslmed.abb3735.
6
Stereotypic neutralizing V antibodies against SARS-CoV-2 spike protein receptor binding domain in patients with COVID-19 and healthy individuals.COVID-19 患者和健康个体中针对 SARS-CoV-2 刺突蛋白受体结合域的刻板中和 V 抗体。
Sci Transl Med. 2021 Jan 27;13(578). doi: 10.1126/scitranslmed.abd6990. Epub 2021 Jan 4.
7
Deep Sequencing of B Cell Receptor Repertoires From COVID-19 Patients Reveals Strong Convergent Immune Signatures.对 COVID-19 患者的 B 细胞受体库进行深度测序揭示了强烈的趋同免疫特征。
Front Immunol. 2020 Dec 15;11:605170. doi: 10.3389/fimmu.2020.605170. eCollection 2020.
8
Alignment free identification of clones in B cell receptor repertoires.无需比对即可鉴定B细胞受体库中的克隆
Nucleic Acids Res. 2021 Feb 26;49(4):e21. doi: 10.1093/nar/gkaa1160.
9
Position-Dependent Differential Targeting of Somatic Hypermutation.位置相关的体细胞超突变的差异靶向。
J Immunol. 2020 Dec 15;205(12):3468-3479. doi: 10.4049/jimmunol.2000496. Epub 2020 Nov 13.
10
Using B cell receptor lineage structures to predict affinity.利用 B 细胞受体谱系结构预测亲和力。
PLoS Comput Biol. 2020 Nov 11;16(11):e1008391. doi: 10.1371/journal.pcbi.1008391. eCollection 2020 Nov.
Zotero 插件