A haplotype-based approach for myotonic dystrophy type 1

Background: Myotonic dystrophy type 1 (DM1) is caused by a CTG repeat expansion in the DMPK gene and represents the most common adult-onset myopathy. Current molecular diagnostics rely on labor-intensive assays that limit accessibility and scalability. Haplotype-based approaches offer a promising alternative for detecting pathogenic expansions indirectly. Methods: We performed genome-wide genotyping in 226 genetically confirmed DM1 patients from the Saguenay-Lac-Saint-Jean founder population and reconstructed haplotypes surrounding the DMPK pathogenic repeat expansion. Based on these haplotypes, we performed a phylogenetic analysis that was further integrated with genealogical reconstruction from the BALSAC database to investigate the origin and transmission of DM1 haplotypes. To evaluate epidemiological utility, we implemented gene dropping simulations within the SLSJ extended genealogies (>80,000 starting individuals) to estimate DM1 incidence at birth. Results: A DM1-associated haplotype was identified in all patients (226/226), consistent with a single major ancestral origin in the SLSJ population. This complete concordance supports the robustness of haplotype-based approaches to infer carrier status without direct repeat sizing. Integrating phylogenetic analysis and genealogical data identified a single couple as the most likely entry point of DM1 in Quebec. Simulation-based estimates of incidence at birth exceeded observed prevalence, suggesting underdiagnosis in the region. Marked geographic heterogeneity in the SLSJ is also observed. Conclusions: Our results demonstrate that haplotype-based approaches can provide a reliable, cost-effective alternative to conventional pathogenic DM1 repeat carriers identification and familial screening strategies.