Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
Computational Bioscience Research Center (CBRC), Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
Genome Biol. 2020 Jun 17;21(1):145. doi: 10.1186/s13059-020-02053-9.
At least 50% of patients with suspected Mendelian disorders remain undiagnosed after whole-exome sequencing (WES), and the extent to which non-coding variants that are not captured by WES contribute to this fraction is unclear. Whole transcriptome sequencing is a promising supplement to WES, although empirical data on the contribution of RNA analysis to the diagnosis of Mendelian diseases on a large scale are scarce.
Here, we describe our experience with transcript-deleterious variants (TDVs) based on a cohort of 5647 families with suspected Mendelian diseases. We first interrogate all families for which the respective Mendelian phenotype could be mapped to a single locus to obtain an unbiased estimate of the contribution of TDVs at 18.9%. We examine the entire cohort and find that TDVs account for 15% of all "solved" cases. We compare the results of RT-PCR to in silico prediction. Definitive results from RT-PCR are obtained from blood-derived RNA for the overwhelming majority of variants (84.1%), and only a small minority (2.6%) fail analysis on all available RNA sources (blood-, skin fibroblast-, and urine renal epithelial cells-derived), which has important implications for the clinical application of RNA-seq. We also show that RNA analysis can establish the diagnosis in 13.5% of 155 patients who had received "negative" clinical WES reports. Finally, our data suggest a role for TDVs in modulating penetrance even in otherwise highly penetrant Mendelian disorders.
Our results provide much needed empirical data for the impending implementation of diagnostic RNA-seq in conjunction with genome sequencing.
全外显子组测序（WES）后，仍有至少 50%的疑似孟德尔疾病患者未得到明确诊断，WES 未捕获的非编码变异在多大程度上导致了这一比例尚不清楚。全转录组测序是 WES 的一种很有前途的补充方法，尽管关于 RNA 分析在大规模孟德尔疾病诊断中的贡献的经验数据还很少。
在这里，我们描述了我们基于 5647 个疑似孟德尔疾病家族的队列中基于转录体有害变异（TDV）的经验。我们首先对所有可以将相应孟德尔表型映射到单个基因座的家族进行检测，以获得 18.9%的 TDV 贡献的无偏估计。我们检查整个队列，发现 TDVs 占所有“已解决”病例的 15%。我们将 RT-PCR 的结果与计算机预测进行比较。来自血液衍生 RNA 的 RT-PCR 获得了绝大多数变异（84.1%）的明确结果，只有一小部分（2.6%）在所有可用 RNA 来源（血液、皮肤成纤维细胞和尿肾上皮细胞衍生）上都无法进行分析，这对 RNA-seq 的临床应用具有重要意义。我们还表明，RNA 分析可以在 155 名接受“阴性”临床 WES 报告的患者中 13.5%的患者中建立诊断。最后，我们的数据表明，TDVs 甚至在其他高度外显的孟德尔疾病中也可以调节外显率。
我们的结果为即将与基因组测序联合实施诊断性 RNA-seq 提供了急需的经验数据。
