Background: Many patients with muscular dystrophies remain genetically undiagnosed despite clinical diagnostic testing including second-generation short read sequencing (SRS) and standard variant analyses of that sequence data.
Objectives: We propose that a significant proportion of these undiagnosed individuals harbor either structural variants (SVs) or cryptic splice sites which are not easily detected by SRS and exome analysis alone. Nanopore long-read sequencing (LRS), a form of third-generation whole genome sequencing, can be used to identify a higher proportion of such SVs and cryptic splice sites in these unsolved families.
Results: We enrolled 11 individuals with muscular dystrophy who lacked complete genetic diagnoses after clinical genetic testing and one asymptomatic individual with a potential DMD duplication. We performed nanopore LRS on genomic DNA samples from these individuals. Nanopore LRS detected likely pathogenic SVs in 3 of these families, in the DMD and LAMA2 genes. Two of these SVs were previously undetected. In addition, we confirmed that the asymptomatic individual harbored a duplication in DMD that was in tandem rather than translocated as initially suspected, and we confirmed a likely pathogenic single nucleotide variant (SNV) in SMCHD1 in another family. Nanopore LRS also detected intronic SNVs in DMD that are predicted to alter splicing in 2 families. All SNVs that were previously detected on clinical genetic testing in these individuals were confirmed on nanopore LRS.
Conclusions: Overall, nanopore LRS identified or confirmed pathogenic variants in all families studied, and identified previously undetected pathogenic SVs and SNVs in 5 of the 11 symptomatic families. This study highlights the utility of nanopore LRS to identify and characterize a broad range of pathogenic variants in individuals with muscular dystrophy, from SNVs to SVs. This technology has the potential to provide a more streamlined means of obtaining complete molecular diagnoses for patients with muscular dystrophy and other Mendelian disorders.