PDF(Pubmed)
Abstract：
BACKGROUND: Dystrophinopathies are the most common X-linked inherited muscle diseases, and the disease-causing gene is DMD. Exonic duplications are a common type of pathogenic variants in the DMD gene, however, 5\' end exonic duplications containing exon 1 are less common. When assessing the pathogenicity of exonic duplications in the DMD gene, consideration must be given to their impact on the reading frame. Traditional molecular methods, such as multiplex ligation-dependent probe amplification (MLPA) and next-generation sequencing (NGS), are commonly used in clinics. However, they cannot discriminate the precise physical locations of breakpoints and structural features of genomic rearrangement. Long-read sequencing (LRS) can effectively overcome this limitation.
RESULTS: We used LRS technology to perform whole genome sequencing on three families and analyze the structural variations of the DMD gene, which involves the duplications of exon 1 and/or exon 2. Two distinct variant types encompassing exon 1 in the DMD Dp427m isoform and/or Dp427c isoform are identified, which have been infrequently reported previously. In pedigree 1, the male individuals harboring duplication variant of consecutive exons 1-2 in the DMD canonical transcript (Dp427m) and exon 1 in the Dp427c transcript are normal, indicating the variant is likely benign. In pedigree 3, the patient carries complex SVs involving exon 1 of the DMD Dp427c transcript showing an obvious phenotype. The locations of the breakpoints and the characteristics of structural variants (SVs) are identified by LRS, enabling the classification of the variants\' pathogenicity.
CONCLUSIONS: Our research sheds light on the complexity of DMD variants encompassing Dp427c/Dp427m promoter regions and emphasizes the importance of cautious interpretation when assessing the pathogenicity of DMD 5\' end exonic duplications, particularly in carrier screening scenarios without an affected proband.
RESULTS: We used LRS technology to perform whole genome sequencing on three families and analyze the structural variations of the DMD gene, which involves the duplications of exon 1 and/or exon 2. Two distinct variant types encompassing exon 1 in the DMD Dp427m isoform and/or Dp427c isoform are identified, which have been infrequently reported previously. In pedigree 1, the male individuals harboring duplication variant of consecutive exons 1-2 in the DMD canonical transcript (Dp427m) and exon 1 in the Dp427c transcript are normal, indicating the variant is likely benign. In pedigree 3, the patient carries complex SVs involving exon 1 of the DMD Dp427c transcript showing an obvious phenotype. The locations of the breakpoints and the characteristics of structural variants (SVs) are identified by LRS, enabling the classification of the variants\' pathogenicity.
CONCLUSIONS: Our research sheds light on the complexity of DMD variants encompassing Dp427c/Dp427m promoter regions and emphasizes the importance of cautious interpretation when assessing the pathogenicity of DMD 5\' end exonic duplications, particularly in carrier screening scenarios without an affected proband.
摘要：
背景：肌营养不良蛋白病是最常见的X连锁遗传性肌肉疾病，致病基因是DMD.外显子重复是DMD基因中常见的致病变异类型，然而,5\'末端包含外显子1的外显子重复不太常见。当评估DMD基因外显子重复的致病性时，必须考虑它们对阅读框架的影响。传统的分子方法,如多重连接依赖性探针扩增（MLPA）和下一代测序（NGS），常用于诊所。然而,它们不能区分断点的精确物理位置和基因组重排的结构特征。长读取测序(LRS)可以有效地克服这种限制。
结果：我们使用LRS技术对三个家族进行了全基因组测序，并分析了DMD基因的结构变异，涉及外显子1和/或外显子2的重复。鉴定了DMDDp427m同种型和/或Dp427c同种型中包含外显子1的两种不同变体类型，以前很少报道。在谱系1中，在DMD规范转录本（Dp427m）和Dp427c转录本中外显子1的连续外显子1-2重复变异的男性个体是正常的，表明该变体可能是良性的。在谱系3中,患者携带涉及DMDDp427c转录物的外显子1的复杂SV,显示明显的表型。断点的位置和结构变体（SV）的特征由LRS识别，能够对变种的致病性进行分类。
结论：我们的研究揭示了包含Dp427c/Dp427m启动子区域的DMD变体的复杂性，并强调了在评估DMD5末端外显子重复的致病性时谨慎解释的重要性。特别是在没有受影响的先证者的承运人筛选方案中。
结果：我们使用LRS技术对三个家族进行了全基因组测序，并分析了DMD基因的结构变异，涉及外显子1和/或外显子2的重复。鉴定了DMDDp427m同种型和/或Dp427c同种型中包含外显子1的两种不同变体类型，以前很少报道。在谱系1中，在DMD规范转录本（Dp427m）和Dp427c转录本中外显子1的连续外显子1-2重复变异的男性个体是正常的，表明该变体可能是良性的。在谱系3中,患者携带涉及DMDDp427c转录物的外显子1的复杂SV,显示明显的表型。断点的位置和结构变体（SV）的特征由LRS识别，能够对变种的致病性进行分类。
结论：我们的研究揭示了包含Dp427c/Dp427m启动子区域的DMD变体的复杂性，并强调了在评估DMD5末端外显子重复的致病性时谨慎解释的重要性。特别是在没有受影响的先证者的承运人筛选方案中。
