NGS-based targeted sequencing identified eight novel variants in patients with Duchenne muscular dystrophy from southwestern China

Abstract

Abstract Background: At present, Multiplex ligation-dependent probe amplification (MLPA) and exome sequencing (ES) are common gene detection methods in patients with Duchenne muscular dystrophy (DMD), but they can not cover the whole genome sequence of DMD gene. In this study, the whole-genome capture of DMD gene and next-generation sequencing (NGS) technology were used to detect the patients with DMD in Southwest China, so as to clarify the application value of this technology and further study the gene mutation spectrum. Methods: From 2017 to 2020, 51 unrelated DMD patients in southwestern China were clinically diagnosed in West China Second University Hospital of Sichuan University (Chengdu, China). The whole-genome of the DMD gene was captured from the peripheral blood of all patients, and next-generation sequencing was performed. Large copy number variants (CNVs) in the exon region of the DMD gene was verified through MLPA, and small variations (such as single nucleotide variation and < 50 bp fragment insertion/deletion) were validated using Sanger sequencing. Results: Among the 51 patients, 49 (96.1%) had pathogenic or likely pathogenic variants in the DMD gene. Among the 49 positive samples, 17 patients (34.7%) had CNVs in the exon region and 32 patients (65.3%) had small variations. A total of eight novel variants were identified: c.10916_10917del, c.1790T>A, c.1842del, c.2461G>T, c.3856G>T, c.5015del, c.5791_5792insCA, and exons 38-50 duplication. Conclusions: Pathogenic or likely pathogenic variants of DMD gene were detected in 49 patients (96.1%), of which 8 variants (16.3%) had not been previously reported. This study not only confirmed the value of NGS-based targeted sequencing for DMD gene but also expanded the gene mutation spectrum of DMD, which may provide effective genetic counseling and prenatal diagnosis for the families.