RNA sequencing solved the most common but unrecognized NEB pathogenic variant in Japanese nemaline myopathy.

Abstract

PURPOSE:

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.

METHODS:

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.

RESULTS:

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.

CONCLUSION:

These results indicated that RNA-seq may be able to solve a large proportion of previously undiagnosed muscle diseases.

• Authors: Kohei Hamanaka, Satoko Miyatake, Eriko Koshimizu, Yoshinori Tsurusaki, Satomi Mitsuhashi, Kazuhiro Iwama, Ahmed N Alkanaq, Atsushi Fujita, Eri Imagawa, Yuri Uchiyama, Nozomu Tawara, Yukio Ando, Yohei Misumi, Mariko Okubo, Mitsuko Nakashima, Takeshi Mizuguchi, Atsushi Takata, Noriko Miyake, Hirotomo Saitsu, Aritoshi Iida, Ichizo Nishino, Naomichi Matsumoto
• Journal: Genetics in medicine : official journal of the American College of Medical Genetics (Genet Med) Vol. 21 Issue 7 Pg. 1629-1638 (07 2019) ISSN: 1530-0366 [Electronic] United States
• PMID: 30467404 (Publication Type: Evaluation Study, Journal Article)

Chemical References

• Muscle Proteins
• nebulin

Topics

• Humans
• Japan
• Muscle Proteins (genetics)
• Muscle, Skeletal (metabolism)
• Mutation
• Myopathies, Nemaline (genetics)
• RNA Splicing
• Sequence Analysis, RNA