Rethinking the pathogenicity of intragenic DMD duplications detected by carrier screening: high prevalence of non-tandem duplications revealed by long-read sequencing

Purpose: The pathogenicity of intragenic duplications depends on their structural configuration. Tandem duplications often disrupt reading frames and cause gene loss-of-function, whereas interspersed (non-tandem) duplications are largely benign. When the configuration cannot be determined, current guidelines presume a tandem structure, leading to some laboratories automatically classifying such variants as likely pathogenic or pathogenic. This study evaluates the validity of this presumption for DMD, in patients with and without clinical indications of dystrophinopathy. Methods: We performed high-coverage whole-genome long-read sequencing on 15 patients with intragenic DMD duplications. Four patients had clinically indicated dystrophinopathy testing, while in the remaining 11 patients, the duplications were detected without clear indications of dystrophinopathy (e.g., "incidentally detected" through carrier screening). Results: All four patients with clinical indications had tandem duplications. In contrast, 64% (7/11) of the incidentally detected cases had interspersed duplications, with four subsequently re-classified as likely benign, two likely pathogenic, and one uncertain. These duplications were often complex, involving co-duplications or co-deletions with other regions. Conclusion: Our findings challenge the presumption that intragenic DMD duplications are predominantly tandem. This highlights the need for a cautious variant interpretation approach, particularly in carrier screening and other settings where variants are identified without indications of dystrophinopathy.