Long-read sequencing identifies complex structural variants in DMD patients

Duchenne muscular dystrophy (DMD) is an X-linked disorder caused by mutations in the DMD gene. Reports of DMD resulting from complex structural variants involving the DMD gene are rare, partly because such variants are often undetectable by standard diagnostic approaches such as multiplex ligation-dependent probe amplification (MLPA) and short-read whole-exome sequencing (WES). Using long-read sequencing, we identified two unrelated pedigrees with complex structural rearrangements affecting the DMD locus. Case 1 carried an inversion encompassing exon 2 of DMD. Case 2 harbored a large-scale inversion of the DMD gene accompanied by two segmental duplications arising as a direct consequence of the inversion; the entire complex allele was maternally inherited. In both instances, simple tandem repeats were present at most of the breakpoints. Our findings demonstrate that long-read sequencing is a powerful tool for resolving complex structural variants. The simple tandem repeats identified at the inversion breakpoints in DMD patients enhance our understanding of the mutational mechanisms underlying structural variation, which in turn aids in developing potential therapeutic strategies.