罕见疾病队列中RNA测序的临床应用和分子见解。

IF 10.4 1区 生物学 Q1 GENETICS & HEREDITY
Jamie C Stark, Neta Pipko, Yijing Liang, Anna Szuto, Chung Ting Tsoi, Megan A Dickson, Kyoko E Yuki, Huayun Hou, Sydney Scholten, Kenzie Pulsifer, Meryl Acker, Meredith Laver, Harsha Murthy, Olivia M Moran, Emily Bonnell, Nicole Liang, Jashanpreet Sidhu, Lucie Dupuis, Mohammad M Ghahramani Seno, Marisa Chard, Rebekah K Jobling, Jessie Cameron, Rose Chami, Michal Inbar-Feigenberg, Michael D Wilson, David A Chitayat, Kym M Boycott, Lianna Kyriakopoulou, Roberto Mendoza-Londono, Christian R Marshall, James J Dowling, Gregory Costain, Ashish R Deshwar
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引用次数: 0

摘要

背景:RNA测序(RNA-seq)正在成为一种有价值的工具,用于识别无法通过单独的dna检测识别的致病RNA转录畸变。先前的研究表明,利用RNA-seq作为罕见先天性遗传病的一线检测方法取得了一些成功。然而,基于dna的检测(越来越多的是全基因组测序)仍然是临床实践中标准的初始检测方法。在患者接受基于dna的测序后,RNA-seq的适应症仍然不明确,这阻碍了广泛的实施和资金/报销。方法:在本研究中,我们确定了四种特定且熟悉的临床场景,并研究了RNA-seq对临床可及组织的诊断效用:(i)澄清假定的内含子或外显子剪接变异(在典型剪接位点之外)的影响,(ii)评估非典型表型患者的典型剪接位点变异,(iii)定义基因内拷贝数变异对基因表达的影响,以及(iv)评估调节元件和基因非翻译区域内的变异。结果:这些假设驱动的RNA-seq分析证实了45%的候选变异参与者的分子诊断和病理机制,为另外21%的DNA发现提供了支持性证据,并允许我们排除另外24%的候选DNA变异。我们产生了支持两种新的孟德尔基因-疾病关联(由PPP1R2和MED14变异引起)和几种新的疾病机制的证据,包括:(1)NFU1非编码变异导致的剪接异构体开关,(2)IDUA转录起始位点变异导致的完全等位基因偏态,以及(3)MAMLD1-BEND2种系基因融合的证据。相比之下,RNA-seq在疑似罕见的先天遗传条件和阴性全基因组测序的个体中只产生了一个新的潜在诊断发现。结论:总的来说,RNA-seq作为一种辅助测试在现实世界的特定临床场景中具有很高的诊断效用。这些发现还强调了RNA-seq揭示与诊断和治疗相关的新型疾病机制的能力。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Clinical applications of and molecular insights from RNA sequencing in a rare disease cohort.

Background: RNA sequencing (RNA-seq) is emerging as a valuable tool for identifying disease-causing RNA transcript aberrations that cannot be identified by DNA-based testing alone. Previous studies demonstrated some success in utilizing RNA-seq as a first-line test for rare inborn genetic conditions. However, DNA-based testing (increasingly, whole genome sequencing) remains the standard initial testing approach in clinical practice. The indications for RNA-seq after a patient has undergone DNA-based sequencing remain poorly defined, which hinders broad implementation and funding/reimbursement.

Methods: In this study, we identified four specific and familiar clinical scenarios, and investigated in each the diagnostic utility of RNA-seq on clinically accessible tissues: (i) clarifying the impact of putative intronic or exonic splice variants (outside of the canonical splice sites), (ii) evaluating canonical splice site variants in patients with atypical phenotypes, (iii) defining the impact of an intragenic copy number variation on gene expression, and (iv) assessing variants within regulatory elements and genic untranslated regions.

Results: These hypothesis-driven RNA-seq analyses confirmed a molecular diagnosis and pathomechanism for 45% of participants with a candidate variant, provided supportive evidence for a DNA finding for another 21%, and allowed us to exclude a candidate DNA variant for an additional 24%. We generated evidence that supports two novel Mendelian gene-disease associations (caused by variants in PPP1R2 and MED14) and several new disease mechanisms, including the following: (1) a splice isoform switch due to a non-coding variant in NFU1, (2) complete allele skew from a transcriptional start site variant in IDUA, and (3) evidence of a germline gene fusion of MAMLD1-BEND2. In contrast, RNA-seq in individuals with suspected rare inborn genetic conditions and negative whole genome sequencing yielded only a single new potential diagnostic finding.

Conclusions: In summary, RNA-seq had high diagnostic utility as an ancillary test across specific real-world clinical scenarios. The findings also underscore the ability of RNA-seq to reveal novel disease mechanisms relevant to diagnostics and treatment.

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来源期刊
Genome Medicine
Genome Medicine GENETICS & HEREDITY-
CiteScore
20.80
自引率
0.80%
发文量
128
审稿时长
6-12 weeks
期刊介绍: Genome Medicine is an open access journal that publishes outstanding research applying genetics, genomics, and multi-omics to understand, diagnose, and treat disease. Bridging basic science and clinical research, it covers areas such as cancer genomics, immuno-oncology, immunogenomics, infectious disease, microbiome, neurogenomics, systems medicine, clinical genomics, gene therapies, precision medicine, and clinical trials. The journal publishes original research, methods, software, and reviews to serve authors and promote broad interest and importance in the field.
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