Departments of Genetics and Pathology, Stanford University, California 94305, USA.
Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA.
Cold Spring Harb Mol Case Stud. 2022 Mar 24;8(2). doi: 10.1101/mcs.a006198. Print 2022 Feb.
In the past 5 years transcriptome or RNA-sequencing (RNA-seq) has steadily emerged as a complementary assay for rare disease diagnosis and discovery. In this perspective, we summarize several recent developments and challenges in the use of RNA-seq for rare disease investigation. Using an accessible patient sample, such as blood, skin, or muscle, RNA-seq enables the assay of expressed RNA transcripts. Analysis of RNA-seq allows the identification of aberrant or outlier gene expression and alternative splicing as functional evidence to support rare disease study and diagnosis. Further, many types of variant effects can be profiled beyond coding variants, as the consequences of noncoding variants that impact gene expression and splicing can be directly observed. This is particularly apparent for structural variants that disproportionately underlie outlier gene expression and for splicing variants in which RNA-seq can both measure aberrant canonical splicing and detect deep intronic effects. However, a major potential limitation of RNA-seq in rare disease investigation is the developmental and cell type specificity of gene expression as a pathogenic variant's effect may be limited to a specific spatiotemporal context and access to a patient's tissue sample from the relevant tissue and timing of disease expression may not be possible. We speculate that as advances in computational methods and emerging experimental techniques overcome both developmental and cell type specificity, there will be broadening use of RNA sequencing and multiomics in rare disease diagnosis and delivery of precision health.
在过去的 5 年中，转录组或 RNA 测序（RNA-seq）作为一种罕见病诊断和发现的补充检测方法逐渐兴起。在本观点中，我们总结了 RNA-seq 在罕见病研究中的一些最新进展和挑战。使用可及的患者样本，如血液、皮肤或肌肉，RNA-seq 能够检测表达的 RNA 转录物。RNA-seq 的分析允许识别异常或异常的基因表达和选择性剪接，作为支持罕见病研究和诊断的功能证据。此外，许多类型的变异效应都可以进行分析，而不仅仅是编码变异，因为影响基因表达和剪接的非编码变异的后果可以直接观察到。这在结构变异中尤为明显，结构变异不成比例地导致异常基因表达，在剪接变异中，RNA-seq 既能测量异常的规范剪接，又能检测深内含子效应。然而，RNA-seq 在罕见病研究中的一个主要潜在局限性是基因表达的发育和细胞类型特异性，因为致病变异的影响可能仅限于特定的时空背景，并且可能无法获得患者组织样本，这些样本来自疾病表达的相关组织和时间。我们推测，随着计算方法的进步和新兴实验技术的出现克服了发育和细胞类型特异性，RNA 测序和多组学在罕见病诊断和精准医疗中的应用将会扩大。
