Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.
Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Kanagawa, Japan.
Genet Med. 2019 Jul;21(7):1629-1638. doi: 10.1038/s41436-018-0360-6. Epub 2018 Nov 23.
The diagnostic rate for Mendelian diseases by exome sequencing (ES) is typically 20-40%. The low rate is partly because ES misses deep-intronic or synonymous variants leading to aberrant splicing. In this study, we aimed to apply RNA sequencing (RNA-seq) to efficiently detect the aberrant splicings and their related variants.
Aberrant splicing in biopsied muscles from six nemaline myopathy (NM) cases unresolved by ES were analyzed with RNA-seq. Variants related to detected aberrant splicing events were analyzed with Sanger sequencing. Detected variants were screened in NM patients unresolved by ES.
We identified a novel deep-intronic NEB pathogenic variant, c.1569+339A>G in one case, and another novel synonymous NEB pathogenic variant, c.24684G>C (p.Ser8228Ser) in three cases. The c.24684G>C variant was observed to be the most frequent among all NEB pathogenic variants in normal Japanese populations with a frequency of 1 in 178 (20 alleles in 3552 individuals), but was previously unrecognized. Expanded screening of the variant identified it in a further four previously unsolved nemaline myopathy cases.
These results indicated that RNA-seq may be able to solve a large proportion of previously undiagnosed muscle diseases.
外显子组测序（ES）对孟德尔疾病的诊断率通常为 20-40%。低诊断率的部分原因是 ES 会遗漏导致异常剪接的深内含子或同义变体。在这项研究中，我们旨在应用 RNA 测序（RNA-seq）来有效地检测异常剪接及其相关变体。
用 RNA-seq 分析了六位肌病（NM）患者的活检肌肉中未通过 ES 解决的异常剪接。用 Sanger 测序分析与检测到的异常剪接事件相关的变体。对 ES 未解决的 NM 患者进行了检测到的变体筛查。
我们在一个病例中发现了一个新的深内含子 NEB 致病性变异，c.1569+339A>G，在三个病例中发现了另一个新的同义 NEB 致病性变异，c.24684G>C（p.Ser8228Ser）。c.24684G>C 变异在正常日本人群中是最常见的所有 NEB 致病性变异之一，频率为 1 比 178（3552 个人中有 20 个等位基因），但以前未被识别。对该变体的扩展筛查在另外四个以前未解决的肌病病例中发现了它。
这些结果表明，RNA-seq 可能能够解决很大一部分以前未确诊的肌肉疾病。
