School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany.
Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany.
Hum Mutat. 2022 Aug;43(8):1056-1070. doi: 10.1002/humu.24416. Epub 2022 Jun 29.
Over the last 5 years, RNA sequencing (RNA-seq) has been established and is increasingly applied as an effective approach complementary to DNA sequencing in molecular diagnostics. Currently, three RNA phenotypes, aberrant expression, aberrant splicing, and allelic imbalance, are considered to provide information about pathogenic variants. By providing a high-throughput, transcriptome-wide functional readout on variants causing aberrant RNA phenotypes, RNA-seq has increased diagnostic rates by about 15% over whole-exome sequencing. This breakthrough encouraged the development of computational tools and pipelines aiming to streamline RNA-seq analysis for implementation in clinical diagnostics. Although a number of studies showed the added value of RNA-seq for the molecular diagnosis of individuals with Mendelian disorders, there is no formal consensus on assessing variant pathogenicity strength based on RNA phenotypes. Taking RNA-seq as a functional assay for genetic variants, we evaluated the value of statistical significance and effect size of RNA phenotypes as evidence for the strength of variant pathogenicity. This was determined by the analysis of 394 pathogenic variants, of which 198 were associated with aberrant RNA phenotypes and 723 benign variants. Overall, this study seeks to establish recommendations for integrating functional RNA-seq data into the the American College of Medical Genetics and Genomics and the Association for Molecular Pathology guidelines classification system.
在过去的 5 年中，RNA 测序（RNA-seq）已经建立并越来越多地应用于分子诊断，作为 DNA 测序的有效补充方法。目前，三种 RNA 表型（异常表达、异常剪接和等位基因失衡）被认为提供了关于致病变异的信息。通过对导致异常 RNA 表型的变异提供高通量、转录组范围的功能读数，RNA-seq 将全外显子组测序的诊断率提高了约 15%。这一突破鼓励开发计算工具和管道，旨在简化 RNA-seq 分析，以便在临床诊断中实施。尽管许多研究表明 RNA-seq 对孟德尔疾病个体的分子诊断具有附加价值，但尚未就基于 RNA 表型评估变异致病性强度达成正式共识。我们将 RNA-seq 作为遗传变异的功能测定，评估了 RNA 表型的统计显著性和效应大小作为变异致病性强度的证据的价值。这是通过对 394 个致病变异的分析来确定的，其中 198 个与异常 RNA 表型相关，723 个良性变异。总的来说，这项研究旨在为将功能 RNA-seq 数据纳入美国医学遗传学和基因组学学院以及分子病理学协会指南分类系统建立建议。
