High-resolution mapping of DMD duplications using long-read sequencing enables precise carrier screening for Duchenne muscular dystrophy

Purpose Exon-level duplications in the DMD gene present interpretive challenges due to limitations in resolving their genomic context. We aimed to assess the utility of long-read genome sequencing (lrGS) in characterizing DMD duplications and guiding clinical interpretation. Methods We applied low coverage lrGS (3–10× depth; ∼8.2 kb mean read length) to 18 individuals with DMD duplications identified via short-read sequencing. Structural variant calling and breakpoint localization were validated by Sanger sequencing. In addition, the genomic characteristics of the duplication breakpoints were systematically analyzed. Results lrGS resolved duplication architecture in all cases. Two duplications (11%, 2/18) were extragenic and reclassified as benign; 16 (89%, 16/18) were tandem events within DMD . Among tandem duplications, 50% (8/16) were classified as pathogenic/likely pathogenic and 50% (8/16) as variants of uncertain significance. Breakpoints were consistently located in intronic regions, often flanked by repetitive elements. Conclusion Low-coverage lrGS enables high-resolution mapping of DMD duplications and improves variant classification. This approach addresses a key gap in carrier screening and molecular diagnosis of dystrophinopathies, and provides lrGS as a prototype for decoding duplication architecture of monogenic disorders, which is a critical advance in genetic diagnosis.