Unique Molecular Identifier-Based High-Resolution HLA Typing and Transcript Quantitation Using Long-Read Sequencing.
Unique Molecular Identifier-Based High-Resolution HLA Typing and Transcript Quantitation Using Long-Read Sequencing.
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DOI：
10.3389/fgene.2022.901377
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发表时间：
2022
影响因子：
3.7
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中科院分区：
文献类型：
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HLA分型为干细胞和实体器官移植提供了必要的结果，也为各种风湿病、胃肠病、神经病学和传染病的诊断提供了益处。越来越清楚的是，了解患者HLA转录本的表达可以为许多相同的患者群体提供额外的益处。我们的研究队列使用长读RNA测序方法进行评估，以提供快速的HLA基因分型结果和规范化的HLA转录物表达。我们使用NGSEngine检测HLA基因分型结果，并使用Athlon2标准化mRNA转录表达。结果表明，该方法的一致性为99.7%。与以往研究相似，在I类基因座中，患者HLA-C的表达明显低于HLA-A和-B （Mann-Whitney U， p值分别为0.0065和0.0154）。总体而言，II类转录本的表达量低于I类转录本。本研究展示了一种使用RNA-Seq的快速高分辨率HLA分型分析方法，该方法可以在7-8小时内提供准确的HLA基因分型和HLA等位基因特异性转录物表达，时间足够短，可以对已故供者进行分析。
HLA typing provides essential results for stem cell and solid organ transplants, as well as providing diagnostic benefits for various rheumatology, gastroenterology, neurology, and infectious diseases. It is becoming increasingly clear that understanding the expression of patient HLA transcripts can provide additional benefits for many of these same patient groups. Our study cohort was evaluated using a long-read RNA sequencing methodology to provide rapid HLA genotyping results and normalized HLA transcript expression. Our assay used NGSEngine to determine the HLA genotyping result and normalized mRNA transcript expression using Athlon2. The assay demonstrated an excellent concordance rate of 99.7%. Similar to previous studies, for the class I loci, patients demonstrated significantly lower expression of HLA-C than HLA-A and -B (Mann–Whitney U, p value = 0.0065 and p value = 0.0154, respectively). In general, the expression of class II transcripts was lower than that of class I transcripts. This study demonstrates a rapid high-resolution HLA typing assay using RNA-Seq that can provide accurate HLA genotyping and HLA allele-specific transcript expression in 7–8 h, a timeline short enough to perform the assay for deceased donors.