Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics
Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics
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DOI：
10.1186/s13059-020-02053-9
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发表时间：
2020-06-17
期刊：
影响因子：
12.3
通讯作者：
Alkuraya, Fowzan
中科院分区：
文献类型：
--
作者：
Maddirevula, Sateesh;Kuwahara, Hiroyuki;Alkuraya, Fowzan
至少有50%的疑似孟德尔疾病患者在全外显子组测序（WES）后仍未确诊，WES未捕获的非编码变体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的一个有前途的补充，尽管关于RNA分析对大规模孟德尔疾病诊断的贡献的经验数据很少。结果在这里，我们描述了我们的经验与转录有害的变异（TDVs）的基础上，一个队列的5647个家庭怀疑孟德尔疾病。我们首先询问所有的家庭，其各自的孟德尔表型可以映射到一个单一的基因座，以获得一个无偏估计的贡献TDVs在18.9%。我们检查了整个队列，发现TDV占所有“解决”病例的15%。我们将RT-PCR的结果与计算机预测进行比较。绝大多数变体（84.1%）的RT-PCR检测结果来自血液来源的RNA，只有少数（2.6%）未能分析所有可用的RNA来源（血液、皮肤成纤维细胞和尿液肾上皮细胞来源），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例接受“阴性”临床WES报告的患者中确定13.5%的诊断。最后，我们的数据表明，即使在其他高度外显的孟德尔疾病中，TDVs也能调节外显率。结论我们的研究结果为即将实施的诊断RNA-seq与基因组测序结合提供了急需的经验数据。
Background 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. Results 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. Conclusions Our results provide much needed empirical data for the impending implementation of diagnostic RNA-seq in conjunction with genome sequencing.