High-resolution repeat structure analysis in myotonic dystrophy type 2 diagnostics using short-read whole genome
Ingrid Lojova1, Marcel Kucharik2, Andrea Zatkova3
1Institute of Clinical and Translational Research, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská Cesta 9, Karlova Ves, 845 05, Bratislava, Slovakia; Comenius University Science Park, Ilkovičova 8, Karlova Ves, 841, 04 Bratislava, Slovakia; Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, Karlova Ves, 841 04, Bratislava, Slovakia.
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).
