https://scholars.lib.ntu.edu.tw/handle/123456789/628632
標題: | Profiling genes encoding the adaptive immune receptor repertoire with gAIRR Suite | 作者: | Lin, Mao-Jan Lin, Yu-Chun Chen, Nae-Chyun Luo, Allen Chilun Lai, Sheng-Kai Hsu, Chia-Lang Jacob Shujui Hsu Chen, Chien-Yu WEI-SHIUNG YANG PEI-LUNG CHEN |
關鍵字: | adaptive immune receptor repertoire (AIRR); allele typing; germline genes encoding AIRR (gAIRR); immunogenomics; novel allele; targeted sequencing | 公開日期: | 2022 | 出版社: | FRONTIERS MEDIA SA | 卷: | 13 | 來源出版物: | Frontiers in Immunology | 摘要: | 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. |
URI: | https://scholars.lib.ntu.edu.tw/handle/123456789/628632 | ISSN: | 1664-3224 | DOI: | 10.3389/fimmu.2022.922513 |
顯示於: | 基因體暨蛋白體醫學研究所 |
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