State Key Laboratory of Reproductive Medicine and Offspring Health, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Jiangsu Province, Nanjing, 210029, China.
Yikon Genomics Company, Ltd, Jiangsu Province, Suzhou, 215000, China.
BMC Genomics. 2024 Mar 19;25(1):292. doi: 10.1186/s12864-024-10224-2.
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.
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.
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.
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 基因中常见的致病性变异类型之一，然而，包含外显子 1 的 5'端外显子重复则较少见。在评估 DMD 基因中外显子重复的致病性时，必须考虑其对阅读框的影响。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），在临床上通常使用。然而，它们无法区分断裂点的精确物理位置和基因组重排的结构特征。长读测序（LRS）可以有效地克服这一限制。
我们使用 LRS 技术对三个家系进行了全基因组测序，并分析了 DMD 基因的结构变异，其中涉及外显子 1 和/或外显子 2 的重复。鉴定出两种不同的变异类型，包含 Dp427m 同工型和/或 Dp427c 同工型中的外显子 1，这些变异类型以前很少报道过。在家系 1 中，携带 DMD 规范转录本（Dp427m）中连续外显子 1-2 和 Dp427c 转录本中外显子 1 的重复变异的男性个体正常，表明该变异可能是良性的。在家系 3 中，患者携带涉及 Dp427c 转录本中外显子 1 的复杂 SVs，表现出明显的表型。通过 LRS 确定了断点的位置和结构变异（SVs）的特征，从而对变异的致病性进行分类。
我们的研究揭示了包含 Dp427c/Dp427m 启动子区域的 DMD 变异的复杂性，并强调了在评估 DMD 5'端外显子重复的致病性时，特别是在没有受影响的先证者的携带者筛查情况下，谨慎解释的重要性。
