High-resolution Repeat Structure Analysis in Myotonic Dystrophy Type 2 Diagnostics Using Short-Read Whole Genome Sequencing

Background/Objectives Diagnostic possibilities for myotonic dystrophy type 2 (DM2) are constantly evolving in order to achieve more accurate and faster diagnosis. Whole genome sequencing (WGS), together with specialized tandem repeat (TR) genotyping bioinformatic tools, represent a breakthrough technology in molecular diagnostics. We decided to characterize new opportunities and challenges in WGS-based DM2 molecular diagnostics. Methods WGS data were obtained from 50 individuals, including five DM2 patients, and one individual carrying a premutation range allele. TR characterization was performed using a modified version of the Dante tool, with results validated by conventional PCR and repeat-primed PCR. Results We used WGS to identify all of the expansion-range DM2 alleles, together with the premutation-range allele. Compared to conventional methods, WGS was more efficient for a detailed sequence structure characterization of the normal-range alleles, and phasing of the entire CNBP-complex motif. A 97 % genotyping concordance rate was achieved between the conventional methods and the WGS-derived results, with discrepancies mainly based on single-repeat differences in the genotypes. The stutter effect introduced some uncertainty in both methods. Conclusion Short-read WGS offers significant potential for DM2 diagnostics by enabling precise repeat motif characterization and may also apply to other tandem repeat disorders (TRDs).